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(-) Description

Title :  IMPROVED STRUCTURE OF THE UNLIGANDED SIMIAN IMMUNODEFICIENCY VIRUS GP120 CORE
 
Authors :  X. Chen, B. Poon, Q. Wang, J. Ma
Date :  14 Jan 09  (Deposition) - 30 Jun 09  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Siv, Aids, Gp120, Structural Refinement, Normal Mode, Apoptosis, Cell Membrane, Envelope Protein, Fusion Protein, Host-Virus Interaction, Membrane, Transmembrane, Virion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Chen, M. Lu, B. K. Poon, Q. Wang, J. Ma
Structural Improvement Of Unliganded Simian Immunodeficienc Virus Gp120 Core By Normal-Mode-Based X-Ray Crystallographi Refinement.
Acta Crystallogr. , Sect. D V. 65 339 2009
PubMed-ID: 19307715  |  Reference-DOI: 10.1107/S0907444909003539

(-) Compounds

Molecule 1 - EXTERIOR MEMBRANE GLYCOPROTEIN GP120
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PSIVGP120CORE
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: PFAST-BAC1
    Fragment: GP120 CORE, RESIDUES 66-109, 209-311, 342-502
    Gene: ENV
    Organism Common: SIV-CPZ
    Organism Scientific: SIMIAN IMMUNODEFICIENCY VIRUS
    Organism Taxid: 11723

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 55)

Asymmetric/Biological Unit (5, 55)
No.NameCountTypeFull Name
1BMA12Ligand/IonBETA-D-MANNOSE
2FUL7Ligand/IonBETA-L-FUCOSE
3MAN12Ligand/IonALPHA-D-MANNOSE
4NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG4Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (55, 55)

Asymmetric Unit (55, 55)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:70BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWAREASN A:211 , THR A:212 , SER A:213 , ILE A:214BINDING SITE FOR RESIDUE NAG A 2
03AC3SOFTWARENAG A:4 , FUL A:6 , BMA A:51 , THR A:245 , ASN A:246BINDING SITE FOR RESIDUE NDG A 3
04AC4SOFTWARENDG A:3 , BMA A:5 , FUL A:6 , BMA A:51 , ARG A:284BINDING SITE FOR RESIDUE NAG A 4
05AC5SOFTWARENAG A:4 , BMA A:51BINDING SITE FOR RESIDUE BMA A 5
06AC6SOFTWARENDG A:3 , NAG A:4 , GLU A:282BINDING SITE FOR RESIDUE FUL A 6
07AC7SOFTWARENDG A:3 , NAG A:4 , BMA A:5BINDING SITE FOR RESIDUE BMA A 51
08AC8SOFTWARENAG A:8 , FUL A:12 , GLN A:269 , ASN A:277 , THR A:461BINDING SITE FOR RESIDUE NAG A 7
09AC9SOFTWARENAG A:7 , BMA A:9BINDING SITE FOR RESIDUE NAG A 8
10BC1SOFTWARENAG A:8 , MAN A:10 , MAN A:11BINDING SITE FOR RESIDUE BMA A 9
11BC2SOFTWAREBMA A:9 , FUL A:18BINDING SITE FOR RESIDUE MAN A 10
12BC3SOFTWAREBMA A:9 , FUL A:22BINDING SITE FOR RESIDUE MAN A 11
13BC4SOFTWARENAG A:7BINDING SITE FOR RESIDUE FUL A 12
14BC5SOFTWARENAG A:14 , FUL A:15 , ASN A:283 , TYR A:303BINDING SITE FOR RESIDUE NDG A 13
15BC6SOFTWARENDG A:13 , FUL A:15BINDING SITE FOR RESIDUE NAG A 14
16BC7SOFTWARENDG A:13 , NAG A:14 , ARG A:284 , LYS A:362BINDING SITE FOR RESIDUE FUL A 15
17BC8SOFTWARENAG A:17 , FUL A:18 , ASN A:294 , TRP A:471BINDING SITE FOR RESIDUE NAG A 16
18BC9SOFTWARENAG A:16 , MAN A:52BINDING SITE FOR RESIDUE NAG A 17
19CC1SOFTWAREMAN A:10 , NAG A:16BINDING SITE FOR RESIDUE FUL A 18
20CC2SOFTWARENAG A:17BINDING SITE FOR RESIDUE MAN A 52
21CC3SOFTWARENAG A:20 , FUL A:22 , ASN A:305BINDING SITE FOR RESIDUE NAG A 19
22CC4SOFTWARENAG A:19 , BMA A:21 , FUL A:22 , TYR A:303BINDING SITE FOR RESIDUE NAG A 20
23CC5SOFTWARENAG A:20BINDING SITE FOR RESIDUE BMA A 21
24CC6SOFTWAREMAN A:11 , NAG A:19 , NAG A:20BINDING SITE FOR RESIDUE FUL A 22
25CC7SOFTWARENAG A:24 , ASN A:370BINDING SITE FOR RESIDUE NDG A 23
26CC8SOFTWARENDG A:23BINDING SITE FOR RESIDUE NAG A 24
27CC9SOFTWARENAG A:26 , FUL A:28 , LYS A:374 , ASN A:376 , VAL A:410BINDING SITE FOR RESIDUE NDG A 25
28DC1SOFTWARENDG A:25 , BMA A:27 , FUL A:28 , NAG A:37BINDING SITE FOR RESIDUE NAG A 26
29DC2SOFTWARENAG A:26 , BMA A:55BINDING SITE FOR RESIDUE BMA A 27
30DC3SOFTWARENDG A:25 , NAG A:26BINDING SITE FOR RESIDUE FUL A 28
31DC4SOFTWAREBMA A:27 , MAN A:56BINDING SITE FOR RESIDUE BMA A 55
32DC5SOFTWAREBMA A:55BINDING SITE FOR RESIDUE MAN A 56
33DC6SOFTWARENAG A:30 , THR A:307 , ASN A:459BINDING SITE FOR RESIDUE NAG A 29
34DC7SOFTWARENAG A:29 , BMA A:31 , THR A:307 , PHE A:345BINDING SITE FOR RESIDUE NAG A 30
35DC8SOFTWARENAG A:30 , BMA A:32 , MAN A:35BINDING SITE FOR RESIDUE BMA A 31
36DC9SOFTWAREBMA A:31 , MAN A:33 , BMA A:34BINDING SITE FOR RESIDUE BMA A 32
37EC1SOFTWAREBMA A:32 , BMA A:34BINDING SITE FOR RESIDUE MAN A 33
38EC2SOFTWAREBMA A:32 , MAN A:33BINDING SITE FOR RESIDUE BMA A 34
39EC3SOFTWAREBMA A:31 , GLY A:346 , ARG A:425 , ARG A:426 , TYR A:428BINDING SITE FOR RESIDUE MAN A 35
40EC4SOFTWARENAG A:37 , ASN A:475BINDING SITE FOR RESIDUE NAG A 36
41EC5SOFTWARENAG A:26 , NAG A:36 , BMA A:38BINDING SITE FOR RESIDUE NAG A 37
42EC6SOFTWARENAG A:37 , MAN A:39 , MAN A:40BINDING SITE FOR RESIDUE BMA A 38
43EC7SOFTWAREBMA A:38 , MAN A:53BINDING SITE FOR RESIDUE MAN A 39
44EC8SOFTWAREBMA A:38BINDING SITE FOR RESIDUE MAN A 40
45EC9SOFTWAREMAN A:39BINDING SITE FOR RESIDUE MAN A 53
46FC1SOFTWARENAG A:42 , FUL A:46 , ASN A:243 , ASP A:244 , THR A:245BINDING SITE FOR RESIDUE NAG A 41
47FC2SOFTWARENAG A:41 , BMA A:43 , MAN A:45BINDING SITE FOR RESIDUE NAG A 42
48FC3SOFTWARENAG A:42 , MAN A:44 , MAN A:45BINDING SITE FOR RESIDUE BMA A 43
49FC4SOFTWAREBMA A:43BINDING SITE FOR RESIDUE MAN A 44
50FC5SOFTWARENAG A:42 , BMA A:43BINDING SITE FOR RESIDUE MAN A 45
51FC6SOFTWARENAG A:41 , ASN A:243 , ASP A:244BINDING SITE FOR RESIDUE FUL A 46
52FC7SOFTWARENAG A:48 , THR A:378 , ALA A:379 , PRO A:380 , ASP A:470 , ASN A:478BINDING SITE FOR RESIDUE NAG A 47
53FC8SOFTWARENAG A:47 , BMA A:49BINDING SITE FOR RESIDUE NAG A 48
54FC9SOFTWARENAG A:48 , MAN A:50BINDING SITE FOR RESIDUE BMA A 49
55GC1SOFTWAREBMA A:49BINDING SITE FOR RESIDUE MAN A 50

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:219
2A:108 -A:210
3A:232 -A:262
4A:242 -A:254
5A:310 -A:343
6A:394 -A:458
7A:401 -A:431

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FUS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FUS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FUS)

(-) Exons   (0, 0)

(no "Exon" information available for 3FUS)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:304
 aligned with Q07374_SIV | Q07374 from UniProtKB/TrEMBL  Length:878

    Alignment length:436
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493      
           Q07374_SIV    64 YSELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCITMRCNKSETDKWGLTKSLTTTAPTAPTAASKIDMVNETSSCITHDNCTGLEQEQMIGCKFNMTGLKRDKTKEYNETWYSTDLVCEQGNSTDNESRCYMNHCNTSIIQESCDKHYWDTIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRRPGNKTVLPVTIMSGLVFHSQPINDRPKQAWCWFGGNWKDAIKEMKQTIVKHPRYTGTNNTDKINLTAPRGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTNQRPKERHRRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAELYRLELGDYKLV 499
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fusA00 A:64-499 HIV Envelope Protein Gp120; Ch                                                                                                ain G                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhh..........ee...------------------------------------------------------------------------------------------------....ee.......---------...................................hhhhh.ee..ee..........eeeee......eeeee....eeeeee..---------------------------.eeeeeehhhhhhhhhhhhhh..............ee............eeee.....eee..hhhhh..................................................ee...eeee..........ee....hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fus A  64 HMELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCIG------------------------------------------------------------------------------------------------AGHCNTSIIQESC---------FRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRGA---------------------------GWCWFGGNWKDAIKEMKQTIVKHPRYTGTNNTDKINLTAPRGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTNQRPKERHRRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAELYRLELGDYKLV 499
                                    73        83        93       103      |  -         -         -         -         -         -         -         -         -         -   |   213     |   -     | 233       243       253       263       273       283       293       303       313         -         -       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493      
                                                                        110                                                                                              207         219       229                                                                                 313                         341
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3FUS)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FUS)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q07374_SIV | Q07374)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q07374_SIV | Q07374: 2bf1

(-) Related Entries Specified in the PDB File

2bf1 THE ORIGINAL UNLIGANDED SIMIAN IMMUNODEFICIENCY VIRUS GP120 CORE STRUCTURE. THIS ENTRY 2B6P REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2BF1SF