index

Porcine Ribonuclease Inhibitor (2BNH)

Jill Kenney

Intro to Structural Bioinformatics;

Spring 2002

Contents

Summary of Porcine Ribonuclease Inhibitor

Crystal Structure

Structural Classification

Structure Comparison

Structural Neighbors

Summary of Porcine Ribonuclease Inhibitor

Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A.

Title: Porcine Ribonuclease Inhibitor

Compound: Mol_Id: 1; Molecule: Ribonuclease Inhibitor; Chain: Null; Synonym: Rnase Inhibitor, Ribonuclease/Angiogenin Inhibitor

Authors: B. Kobe, J. Deisenhofer

Exp. Method: X-ray Diffraction

Classification: Acetylation

Source: Sus scrofa

Primary Citation: Kobe, B., Deisenhofer, J.: Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. J Mol Biol 264 pp. 1028 (1996)
[ Medline ]

Deposition Date: 29-Jun-1996 Release Date: 12-Mar-1997

Resolution [Å]: 2.30 R-Value: 0.200

Space Group: I 4

Unit Cell:

dim [Å]: a 134.90 b 134.90 c 83.60

angles [¯]: alpha 90.00 beta 90.00 gamma 90.00

Polymer Chains: 2BNH Residues: 457

Atoms: 3478

HET groups:

ID Name Formula

ACE ACETYL GROUP C₂H₃O

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Crystal Structure

Here's the structure in Chime

The Medline file can be found here.

This structure has been deposited in the Protein Data Bank under the code 2BNH. This structure was determined by X-ray diffraction to a resolution of 2.3 Å. Refined with the X-plor program.

Resolution [Å]: 2.30

R-Value: 0.200

Space Group: I 4

Unit Cell:

dim [Å]: a 134.90 b 134.90 c 83.60
angles [¯]: alpha 90.00 beta 90.00 gamma 90.00

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Structural Classification

SCOP (Structural Classification of Proteins)

Class: Alpha and beta proteins (a/b); Mainly parallel beta sheets (beta-alpha-beta units)

Fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) 2 curved layers, a/b; parallel beta-sheet; order 1234...N

Superfamily: RNI-like regular structure consisting of similar repeats

Family: Ribonuclease inhibitor

Protein: Ribonuclease inhibitor duplication: consists of 16 repeats

Species: Pig (Sus scrofa)

CATH (Class, Architecture, Topology, Homology)

Class: Alpha Beta

Architecture: Horseshoe

Topology: Ribonuclease Inhibitor

Homology: Acetylation

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Structure Comparison

2BNH 1A4Y

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Structural Neighbors

CATH

Found 1 related domain

Domain CATH code Length Image

2bnh00 3.80.10.10 456

A whole lot of neighbors

FSSP

1 matches were found

PDBid Repre Rmsd Lali Lseq %ide Compound
2bnh 1a4yA 1.2 456 456 77 ribonuclease inhibitor (rnase inhibitor, ribonucleaseAN

SCOP

PDB Entry Domains:

1.2bnh
     complexed with ace
2.1dfj
     complexed with ace, so4
         1.chain i

VAST

A whole lot of neighbors

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Multiple Sequence Alignment

CE Alignment Results

Structure Alignment - 2BNH:_ Neighbors

Sequence alignment based on assembled pairwise structure alignments between 2BNH:_ and its neighbors. Light color indicates not-aligned residues in structural neighbors. Position numbers according to sequence (starting from 1) and according to PDB are given as SSSS/PPPP, SSSS - sequence, PPPP - PDB.




  2BNH:_    2/2     MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRT
  1A4Y:D    5/6     QSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRS
  1YRG:A    1/3     -----------------------------------------------------ARFSIEG
  1FQV:C            ------------------------------------------------------------
  1XUM:_            ------------------------------------------------------------
  1LUT:_            ------------------------------------------------------------


  2BNH:_   62/62    NELGDAGVHL-----VLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHL
  1A4Y:D   65/66    NELGDVGVHC-----VLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHL
  1YRG:A    8/10    KSLKLDAITTEDEKSVFAVLLE-DDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEF
  1FQV:C   17/118   -------------------------------------------------LLGIFSCLCL-
  1XUM:_            ------------------------------------------------------------
  1LUT:_            ------------------------------------------------------------


  2BNH:_  117/117   SDNPL------GDAGLRLLCE------GLLDPQCHLEKLQLEYCRLTAASCEPLASVLRA
  1A4Y:D  120/121   SDNLL------GDAGLQLLCE------GLLDPQCRLEKLQLEYCSLSAASCEPLASVLRA
  1YRG:A   67/69    SDIFTGRVKDEIPEALRLLLQ------ALL-KCPKLHTVRLSDNAFGPTAQEPLIDFLSK
  1FQV:C   27/128   --------------PELLKVSGVCKRWYRLASDESLWQTLDLTGKNLH--PDVTGRLLSQ
  1XUM:_            ------------------------------------------------------------
  1LUT:_            ------------------------------------------------------------


  2BNH:_  165/165   TRALKELTVSNNDIGEAGARVLGQGLADSA--------CQLETLRLENCGLTPANCKDLC
  1A4Y:D  168/169   KPDFKELTVSNNDINEAGVRVLCQGLKDSP--------CQLEALKLESCGVTSDNCRDLC
  1YRG:A  120/122   HTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWA
  1FQV:C   71/172   --GVIAFRCPRSFMDQPLAE---HFSP-----------FRVQHMDLSNSVIEVSTLHGIL
  1XUM:_    1/55    ---TQTLKLIETHL----RTIPSHAFSNL---------PNISRIYVSIDVTLQQLES---
  1LUT:_    1/52    ---LTRLSLAYLPV----KVIPSQAFRGL---------NEVIKIEISQIDSLERIEA---


  2BNH:_  217/217   GIVASQASLRELDLGSNGLGDAGIAEL-CPGLLSPASRLKTLWLWECDITASGCRDLCRV
  1A4Y:D  220/221   GIVASKASLRELALGSNKLGDVGMAEL-CPGLLHPSSRLRTLWIWECGITAKGCGDLCRV
  1YRG:A  180/182   KTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAY-CQELKVLDLQDNTFTHLGSSALAIA
  1FQV:C  115/216   SQCS---KLQNLSLEGLRLSDPIV-NT-LAKN----SNLVRLNLSGCSG--FSEFALQTL
  1XUM:_   42/96    HSFYNLSKVTHIEIRNTRNLTYI--DP-DALKEL--PLLKSLAFSNTGL-KMFPD-LTKV
  1LUT:_   42/93    NAFDNLLNLSEILIQNTKNLRYI--EP-GAFINL--PRLKYLSICNTGI-RKFPD-VTKV


  2BNH:_  276/276   LQAKETLKELSLAGNK-LGDEGARLLCESLLQPGCQ-LESLWVKSCSLTAACCQHVSLML
  1A4Y:D  279/280   LRAKESLKELSLAGNE-LGDEGARLLCETLLEPGCQ-LESLWVKSCSFTAACCSHFSSVL
  1YRG:A  239/241   LKSWPNLRELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVI
  1FQV:C  164/265   LSSCSRLDELNLSWCFDFTEKHVQVAVAHV---SET-ITQLNLS-GYRKNLQKSDLSTLV
  1XUM:_   95/149   YST-DIFFILEITDNP-YMTSIP---VNAFQGLCNE-TLTLKLYNNGF-TSVQGYDFFGT
  1LUT:_   95/146   FSS-ESNFILEICDNL-HITTIP---GNAFQGMNNE-SVTLKLYGNGF-EEVQSHAFNGT


  2BNH:_  334/334   TQNKH-LLELQLSSNKLGDSGIQELCQALSQPG-TT----LRVLCLGDCEVTNSGCSSLA
  1A4Y:D  337/338   AQNRF-LLELQISNNRLEDAGVRELCQGLGQPG-SV----LRVLWLADCDVSDSSCSSLA
  1YRG:A  298/300   DEKMPDLLFLELNGNRFSEED-DVVDEIRE----VFSTRGRGELDELDD-----------
  1FQV:C  219/320   RRCPN-LVHLDLSDSVM---LKNDCFQEFFQ-L-NY----LQHLSLSRCYD--IIPETLL
  1XUM:_  148/202   ----K-LDAVYLNKNKYLTVIDK---DAFGG-VYSG----PSLLDVSQT-----------
  1LUT:_  148/199   ----T-LTSLELKENVHLEKMHN---GAFRG-A-TG----PKTLDISST-----------


  2BNH:_  388/388   SLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALE
  1A4Y:D  391/392   ATLLANHSLRELDLSNNCLGDAGILQLVESVRQPGCLLEQLVLYDIYWSEEMEDRLQALE
  1YRG:A            ------------------------------------------------------------
  1FQV:C  267/368   ELG-EIPTLKTLQVFGIVPDGTLQLLKEALP------HLQINCSH---------------
  1XUM:_            ------------------------------------------------------------
  1LUT:_            ------------------------------------------------------------


  2BNH:_  448/448   GSKPGLRVIS
  1A4Y:D  451/452   KDKPSLRVIS
  1YRG:A            ----------
  1FQV:C            ----------
  1XUM:_            ----------
  1LUT:_            ----------

1A4Y:D

1.2	77.2
456	8.1

1YRG:A

2.5	20.3
315	7.3

2.5	17.8
315	-1.0

1FQV:C

3.8	14.6
281	6.8

3.7	13.2
281	-1.0

3.8	12.6
230	-1.0

1XUM:_

1.9	8.2
182	6.6

2.0	8.2
182	-1.0

2.4	16.2
179	-1.0

3.2	12.8
164	-1.0

1LUT:_

1.9	13.2
182	6.6

2.0	14.3
182	-1.0

2.4	16.8
179	-1.0

3.2	12.8
164	-1.0

0.3	45.6
182	-1.0

2BNH:_

1A4Y:D

1YRG:A

1FQV:C

1XUM:_

Each cell in distance matrix provides:
RMSD(Å) Sequence identity(%)
Length of alignment Z-score

ClustalW Alignment Results

CLUSTAL W (1.82) Multiple Sequence Alignments



Sequence format is Pearson
Sequence 1: 2BNH__          457 aa
Sequence 2: 1YRG_A          385 aa
Sequence 3: 1XUM__          183 aa
Sequence 4: 1FQV_A          336 aa
Sequence 5: 1LUT__          182 aa
Sequence 6: 1A4Y_A          460 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  14
Sequences (1:3) Aligned. Score:  4
Sequences (1:4) Aligned. Score:  9
Sequences (1:5) Aligned. Score:  8
Sequences (1:6) Aligned. Score:  77
Sequences (2:3) Aligned. Score:  3
Sequences (2:4) Aligned. Score:  10
Sequences (2:5) Aligned. Score:  9
Sequences (2:6) Aligned. Score:  11
Sequences (3:4) Aligned. Score:  7
Sequences (3:5) Aligned. Score:  45
Sequences (3:6) Aligned. Score:  5
Sequences (4:5) Aligned. Score:  7
Sequences (4:6) Aligned. Score:  9
Sequences (5:6) Aligned. Score:  4
Guide tree        file created:   [/ebi/extserv/old-work/72014.43763-7429.dnd]
Start of Multiple Alignment
There are 5 groups
Aligning...
Group 1: Sequences:   2      Score:8893
Group 2:                     Delayed
Group 3:                     Delayed
Group 4: Sequences:   2      Score:2838
Group 5: Sequences:   4      Score:1305
Sequence:2     Score:2196
Sequence:4     Score:1887
Alignment Score 1986
CLUSTAL-Alignment file created  [/ebi/extserv/old-work/72014.43763-7429.aln]

Your Multiple Sequence Alignment

72014.43763-7429.aln

CLUSTAL W (1.82) multiple sequence alignment


2BNH__          ---XMNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTEL 57
1A4Y_A          SLDIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAEL 60
1XUM__          ----------------------------------------TQTLKLIETHLRTIPSHAFS 20
1LUT__          ----------------------------------------LTRLSLAYLPVKVIPSQAFR 20
1YRG_A          ------------------------ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEI 36
1FQV_A          ---------------------------RENFPGVSWDSLPDELLLGIFSCLCLPELLKVS 33
                     . .  ... :.:  :.  .     .    .  . .          :         

2BNH__          CLRTNELGDAGVHLVLQGLQSPTCK-IQKLSLQNCSLTEAGC----GVLPSTLRSLPTLR 112
1A4Y_A          NLRSNELGDVGVHCVLQGLQTPSCK-IQKLSLQNCCLTGAGC----GVLSSTLRTLPTLQ 115
1XUM__          NLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLT----YIDPDALKELPLLK 76
1LUT__          GLNEVIKIEISQIDSLERIEANAFDNLLNLSEILIQNTKNLR----YIEPGAFINLPRLK 76
1YRG_A          VLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLH 96
1FQV_A          GVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFR-----CPRSFMDQPLAE 88
                 :        .     : :         ..:                    ::   *  .

2BNH__          ELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELT 172
1A4Y_A          ELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELT 175
1XUM__          SLAFSN-----TGLKMFPD------------------LTKVYSTDIFFILEITDNPYMTS 113
1LUT__          YLSICN-----TGIRKFPD------------------VTKVFSSESNFILEICDNLHITT 113
1YRG_A          TVRLSDNAFGPTAQEPLID-------------------FLSKHTPLEHLYLHNNGLGPQA 137
1FQV_A          HFSPFR-----VQHMDLSN-------------------SVIEVSTLHGILSQCSKLQNLS 124
                 .    .  . .    : :.  ....  .. . . .            :          :

2BNH__          VSNNDIGEAGARVLGQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLR-ELDLG 231
1A4Y_A          VSNNDINEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKASLR-ELALG 234
1XUM__          IPVN---------AFQGLCN---ETLTLKLYNNGFTSVQGYDFFGTKLDAVYLNKNKYLT 161
1LUT__          IPGN---------AFQGMNN---ESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLE 161
1YRG_A          GAKIAR--ALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLH-TVKMV 194
1FQV_A          LEGLRLS----DPIVNTLAK---NSNLVRLNLSGCSGFSEFALQTLLSSCSRLD---ELN 174
                      ..:      :   ...     :          .             *     : 

2BNH__          SNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNK 291
1A4Y_A          SNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNE 294
1XUM__          VIDKDAFGGVYSGPSLLDVSQT-------------------------------------- 183
1LUT__          KMHNGAFRGA-TGPKTLDISST-------------------------------------- 182
1YRG_A          QNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCL 254
1FQV_A          LSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQ-KSDLSTLVRRCPNLVHLDLSDSV 233
                                   ..            .  .    .       .    .  .  

2BNH__          LGDEGARLLCESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGD 351
1A4Y_A          LGDEGARLLCETLLEPGCQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNNRLED 354
1XUM__          ------------------------------------------------------------
1LUT__          ------------------------------------------------------------
1YRG_A          LSARGAAAVVDAFSK---------------------------LENIGLQTLRLQYNEIEL 287
1FQV_A          MLKN------------------------------------------DCFQEFFQLNYLQH 251
                    .:    .:  ..... .:   .:.: :::...  :    ..        . .    

2BNH__          SGIQELCQALSQPGTTLRVLCLGDCEVTN-SGCSSLASLLLANRSLRELDLSNNCVGDPG 410
1A4Y_A          AGVRELCQGLGQPGSVLRVLWLADCDVSD-SSCSSLAATLLANHSLRELDLSNNCLGDAG 413
1XUM__          ------------------------------------------------------------
1LUT__          ------------------------------------------------------------
1YRG_A          DAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEELTD 347
1FQV_A          LSLSRCYDIIPETLLELG--EIPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIA 309
                 .         .                .  .          . .    .   .      

2BNH__          VLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS 457
1A4Y_A          ILQLVESVRQPGCLLEQLVLYDIYWSEEMEDRLQALEKDKPSLRVIS 460
1XUM__          -----------------------------------------------
1LUT__          -----------------------------------------------
1YRG_A          EEEEDEEEEAESQSPEPETS-----EEEKEDKELADELSKAHI---- 385
1FQV_A          RPTIGNKKNQ-----------------EIWGIKCRLTLQKPSCL--- 336
                      .    .   .     .    ..  .       ...     :

Your guide tree

72014.43763-7429.dnd

(
(
(
2BNH__:0.10787,
1A4Y_A:0.12189)
:0.32288,
1YRG_A:0.42847)
:0.02489,
(
1XUM__:0.28358,
1LUT__:0.26038)
:0.20901,
1FQV_A:0.44230);

Conclusion:

It seems that 2BNH is most similar to 1A4Y. This makes sense because after checking 1A4Y in the PDB t appears to be the equivalent for the ribonuclease inhibitor for Homo Sapiens. Here is the summary of 1A4Y in the PDB:

Title:

Ribonuclease Inhibitor-Angiogenin Complex

Compound:

Mol_Id: 1; Molecule: Ribonuclease Inhibitor; Chain: A, D
Mol_Id: 2; Molecule: Angiogenin; Chain: B, E; Ec: 3.1.27.-; Engineered: Yes

Authors:

A. C. Papageorgiou, K. R. Acharya

Exp. Method:

X-ray Diffraction

Classification:

Complex (Inhibitor/Nuclease)

EC Number:

3.1.27.-

Source:

Homo sapiens

Primary Citation:

Papageorgiou, A. C., Shapiro, R., Acharya, K. R.: Molecular recognition of human angiogenin by placental ribonuclease inhibitor--an X-ray crystallographic study at 2.0 A resolution. EMBO J 16 pp. 5162 (1997)
[ Medline ]

Deposition Date:

08-Feb-1998

Release Date:

14-Oct-1998

Resolution [Å]:

2.00

R-Value:

0.193

Space Group:

P 1 21 1

Unit Cell:

dim [Å]:	a	66.55	b	105.61	c	93.52
angles [¯]:	alpha	90.00	beta	107.09	gamma	90.00

Last Revised: May 6, 2002