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(-) Description

Title :  STRUCTURE OF AN UNLIGANDED AND FULLY-GLYCOSYLATED SIV GP120 ENVELOPE GLYCOPROTEIN
 
Authors :  B. Chen, E. M. Vogan, H. Gong, J. J. Skehel, D. C. Wiley, S. C. Harrison
Date :  02 Dec 04  (Deposition) - 17 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Virus Protein, Siv, Gp120, Envelope Glycoprotein, Aids, Coat Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Chen, E. M. Vogan, H. Gong, J. J. Skehel, D. C. Wiley, S. C. Harrison
Structure Of An Unliganded Simian Immunodeficiency Virus Gp120 Core
Nature V. 433 834 2005
PubMed-ID: 15729334  |  Reference-DOI: 10.1038/NATURE03327
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXTERIOR MEMBRANE GLYCOPROTEIN GP120
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Plasmid: PSIVGP120CORE
    Expression System Taxid: 7111
    Expression System Vector: PFAST-BAC1
    Fragment: GP120 CORE, RESIDUES 66-109,209-311,342-502
    Organism Common: SIV
    Organism Scientific: SIMIAN IMMUNODEFICIENCY VIRUS
    Organism Taxid: 11723
    Strain: MAC32H
    Synonym: SIV GP120

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 50)

Asymmetric/Biological Unit (5, 50)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2FUC7Ligand/IonALPHA-L-FUCOSE
3MAN11Ligand/IonALPHA-D-MANNOSE
4NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG6Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (50, 50)

Asymmetric Unit (50, 50)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:70BINDING SITE FOR RESIDUE NAG A1500
02AC2SOFTWAREASN A:211 , SER A:213BINDING SITE FOR RESIDUE NAG A1501
03AC3SOFTWARENDG A:1502 , BMA A:1504BINDING SITE FOR RESIDUE NAG A1503
04AC4SOFTWARENDG A:1502 , NAG A:1503BINDING SITE FOR RESIDUE BMA A1504
05AC5SOFTWARETHR A:245 , ASN A:246 , TYR A:288 , NAG A:1503 , BMA A:1504 , FUC A:1505BINDING SITE FOR RESIDUE NDG A1502
06AC6SOFTWAREGLU A:282 , ARG A:284 , NDG A:1502BINDING SITE FOR RESIDUE FUC A1505
07AC7SOFTWAREGLN A:269 , ASN A:277 , NAG A:1507 , FUC A:1511BINDING SITE FOR RESIDUE NAG A1506
08AC8SOFTWARENAG A:1506 , BMA A:1508 , NAG A:1528BINDING SITE FOR RESIDUE NAG A1507
09AC9SOFTWARENAG A:1507 , MAN A:1509 , MAN A:1510BINDING SITE FOR RESIDUE BMA A1508
10BC1SOFTWAREBMA A:1508 , FUC A:1517BINDING SITE FOR RESIDUE MAN A1509
11BC2SOFTWAREBMA A:1508 , FUC A:1521BINDING SITE FOR RESIDUE MAN A1510
12BC3SOFTWARENAG A:1506BINDING SITE FOR RESIDUE FUC A1511
13BC4SOFTWARENDG A:1512 , FUC A:1514BINDING SITE FOR RESIDUE NAG A1513
14BC5SOFTWAREASN A:283 , NAG A:1513 , FUC A:1514BINDING SITE FOR RESIDUE NDG A1512
15BC6SOFTWAREARG A:284 , NDG A:1512 , NAG A:1513BINDING SITE FOR RESIDUE FUC A1514
16BC7SOFTWARENDG A:1515BINDING SITE FOR RESIDUE NAG A1516
17BC8SOFTWAREASP A:293 , ASN A:294 , TRP A:471 , NAG A:1516 , FUC A:1517BINDING SITE FOR RESIDUE NDG A1515
18BC9SOFTWAREMAN A:1509 , NDG A:1515BINDING SITE FOR RESIDUE FUC A1517
19CC1SOFTWAREASN A:305 , NAG A:1519 , FUC A:1521BINDING SITE FOR RESIDUE NAG A1518
20CC2SOFTWARETYR A:303 , NAG A:1518 , BMA A:1520 , FUC A:1521BINDING SITE FOR RESIDUE NAG A1519
21CC3SOFTWARENAG A:1519BINDING SITE FOR RESIDUE BMA A1520
22CC4SOFTWAREMAN A:1510 , NAG A:1518 , NAG A:1519BINDING SITE FOR RESIDUE FUC A1521
23CC5SOFTWARENDG A:1522BINDING SITE FOR RESIDUE NAG A1523
24CC6SOFTWAREASN A:370 , NAG A:1523BINDING SITE FOR RESIDUE NDG A1522
25CC7SOFTWARENDG A:1524 , BMA A:1526 , FUC A:1527 , NAG A:1536BINDING SITE FOR RESIDUE NAG A1525
26CC8SOFTWARENAG A:1525BINDING SITE FOR RESIDUE BMA A1526
27CC9SOFTWARELYS A:374 , ASN A:376 , VAL A:410 , NAG A:1525 , FUC A:1527 , NDG A:1546BINDING SITE FOR RESIDUE NDG A1524
28DC1SOFTWARENDG A:1524 , NAG A:1525BINDING SITE FOR RESIDUE FUC A1527
29DC2SOFTWARETHR A:307 , ASN A:459 , NAG A:1507 , NAG A:1529BINDING SITE FOR RESIDUE NAG A1528
30DC3SOFTWARETHR A:307 , PHE A:345 , GLY A:346 , NAG A:1528 , BMA A:1530BINDING SITE FOR RESIDUE NAG A1529
31DC4SOFTWARENAG A:1529 , MAN A:1531 , MAN A:1534BINDING SITE FOR RESIDUE BMA A1530
32DC5SOFTWAREBMA A:1530 , MAN A:1532 , MAN A:1533BINDING SITE FOR RESIDUE MAN A1531
33DC6SOFTWARETRP A:405 , ARG A:425 , MAN A:1531 , MAN A:1533BINDING SITE FOR RESIDUE MAN A1532
34DC7SOFTWAREGLY A:347 , ARG A:426 , TYR A:428 , BMA A:1530BINDING SITE FOR RESIDUE MAN A1534
35DC8SOFTWAREMAN A:1531 , MAN A:1532BINDING SITE FOR RESIDUE MAN A1533
36DC9SOFTWARELYS A:374 , GLY A:474 , ASN A:475 , NAG A:1536BINDING SITE FOR RESIDUE NAG A1535
37EC1SOFTWARENAG A:1525 , NAG A:1535 , BMA A:1537 , MAN A:1538BINDING SITE FOR RESIDUE NAG A1536
38EC2SOFTWARENAG A:1536 , MAN A:1538 , MAN A:1539BINDING SITE FOR RESIDUE BMA A1537
39EC3SOFTWARENAG A:1536 , BMA A:1537BINDING SITE FOR RESIDUE MAN A1538
40EC4SOFTWAREBMA A:1537BINDING SITE FOR RESIDUE MAN A1539
41EC5SOFTWARECYS A:242 , ASN A:243 , ASP A:244 , VAL A:258 , NAG A:1541 , FUC A:1545BINDING SITE FOR RESIDUE NAG A1540
42EC6SOFTWARENAG A:1540 , BMA A:1542 , MAN A:1544 , FUC A:1545BINDING SITE FOR RESIDUE NAG A1541
43EC7SOFTWARENAG A:1541 , MAN A:1543 , MAN A:1544BINDING SITE FOR RESIDUE BMA A1542
44EC8SOFTWAREBMA A:1542BINDING SITE FOR RESIDUE MAN A1543
45EC9SOFTWARENAG A:1541 , BMA A:1542BINDING SITE FOR RESIDUE MAN A1544
46FC1SOFTWAREASN A:243 , ASP A:244 , NAG A:1540 , NAG A:1541BINDING SITE FOR RESIDUE FUC A1545
47FC2SOFTWAREASN A:475 , GLN A:476 , NDG A:1546 , BMA A:1548BINDING SITE FOR RESIDUE NAG A1547
48FC3SOFTWARENAG A:1547 , MAN A:1549BINDING SITE FOR RESIDUE BMA A1548
49FC4SOFTWAREBMA A:1548BINDING SITE FOR RESIDUE MAN A1549
50FC5SOFTWARETHR A:378 , ALA A:379 , PRO A:380 , ASP A:470 , GLN A:476 , ASN A:478 , THR A:480 , NDG A:1524 , NAG A:1547BINDING SITE FOR RESIDUE NDG A1546

(-) 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 2BF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BF1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BF1)

(-) Exons   (0, 0)

(no "Exon" information available for 2BF1)

(-) 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 ENV_SIVMK | P05884 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:439
                                    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         
            ENV_SIVMK    64 YSELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCITMRCNKSETDRWGLTKSSTTITTAAPTSAPVSEKIDMVNETSSCIAQNNCTGLEQEQMISCKFTMTGLKRDKTKEYNETWYSTDLVCEQGNSTDNESRCYMNHCNTSVIQESCDKHYWDTIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRRPGNKTVLPVTIMSGLVFHSQPLTDRPKQAWCWFGGKWKDAIKEVKQTIVKHPRYTGTNNTDKINLTAPGGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTTQRPKERHRRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTSITMSAEVAELYRLELGDYKLV 502
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2bf1A00 A:64-499 HIV Envelope Protein Gp120; Ch                                                                                                   ain G                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhh......eeeeee...---------------------------------------------------------------------------------------------------....eeeeee...---------.........eeeee.............eeeeee...hhhheeee............eeeee.......eeeeee..eeeeeee..---------------------------eeeeeeehhhhhhhhhhhhhhhh.........eeee...........eeeeeee...eeeee.hhhh..eeee..............eeeeee..eeeee...eeeee........eeeeeeeeeeeeeee....eeeeee...hhhhhhhhh...eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bf1 A  64 HMELALNVTESFDAWENTVTEQAIEDVWQLFETSIKPCVKLSPLCIG---------------------------------------------------------------------------------------------------AGHCNTSIIQESC---------FRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKYYNLTMKCRGA---------------------------GWCWFGGNWKDAIKEMKQTIVKHPRYTGTNNTDKINLTAPRGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRDVTNQRPKERHRRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAELYRLELGDYKLV 499
                                    73        83        93       103      |  -         -         -         -         -         -         -         -         -         -      |210        |-       230       240       250       260       270       280       290       300       310  |      -         -         -|      350       360       370       380       390       400       410       420       430       440       450       460       470       480       490         
                                                                        110                                                                                                 207         219       229                                                                                 313                         341                                                                                                                                                              


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 2bf1A00 A:64-499 HIV Envelope Protein Gp120; Ch                                                                                                ain G                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhh......eeeeee...------------------------------------------------------------------------------------------------....eeeeee...---------.........eeeee.............eeeeee...hhhheeee............eeeee.......eeeeee..eeeeeee..---------------------------eeeeeeehhhhhhhhhhhhhhhh.........eeee...........eeeeeee...eeeee.hhhh..eeee..............eeeeee..eeeee...eeeee........eeeeeeeeeeeeeee....eeeeee...hhhhhhhhh...eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bf1 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 2BF1)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BF1)

(-) Gene Ontology  (14, 28)

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.

Chain A   (ENV_SIVMK | P05884)
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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  2bf1
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  Q07374_SIV | Q07374
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 Related Entries

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        Q07374_SIV | Q07374: 3fus

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