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(-) Description

Title :  CRYSTAL STRUCTURE OF FULLY GLYCOSYLATED HIV-1 GP120 CORE BOUND TO CD4 AND 17B FAB
 
Authors :  L. Kong, I. A. Wilson, P. D. Kwong
Date :  05 Nov 14  (Deposition) - 31 Dec 14  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.49
Chains :  Asym. Unit :  B,C,D,G
Biol. Unit 1:  B,C,D,G  (1x)
Biol. Unit 2:  B (1x),C (1x),D (1x),G (1x)
Keywords :  Immunoglobulin Fold, N-Linked Glycosylation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kong, I. A. Wilson, P. D. Kwong
Crystal Structure Of A Fully Glycosylated Hiv-1 Gp120 Core Reveals A Stabilizing Role For The Glycan At Asn262.
Proteins V. 83 590 2015
PubMed-ID: 25546301  |  Reference-DOI: 10.1002/PROT.24747

(-) Compounds

Molecule 1 - 2-DOMAIN CD4
    Chains: B
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Taxid: 10029
    Expression System Tissue: OVARY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 17B FAB LIGHT CHAIN
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Expression System Tissue: KIDNEY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - 17B FAB HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Expression System Tissue: KIDNEY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - HIV-1 YU2 GP120 CORE CHIMERIC PROTEIN
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Taxid: 9606
    Expression System Tissue: KIDNEY
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (ISOLATE YU2)
    Organism Taxid: 362651

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : BCDG
Biological Unit 1 (1x): BCDG
Biological Unit 2 (1x): B (1x)C (1x)D (1x)G (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric Unit (3, 27)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 27)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 27)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU G:211 , PRO G:212 , VAL G:254 , ASN G:262 , ASN G:377 , CYS G:445 , SER G:447 , NAG G:502BINDING SITE FOR RESIDUE NAG G 501
02AC2SOFTWAREPHE G:210 , GLY G:379 , CYS G:445 , SER G:446 , NAG G:501 , BMA G:503 , MAN G:505 , NAG G:519BINDING SITE FOR RESIDUE NAG G 502
03AC3SOFTWAREPRO G:206 , NAG G:502 , MAN G:504 , MAN G:506BINDING SITE FOR RESIDUE BMA G 503
04AC4SOFTWAREBMA G:503 , MAN G:505 , MAN G:509BINDING SITE FOR RESIDUE MAN G 504
05AC5SOFTWAREARG G:444 , NAG G:502 , MAN G:504 , NAG G:524BINDING SITE FOR RESIDUE MAN G 505
06AC6SOFTWAREPRO G:206 , LYS G:207 , SER G:209 , ILE G:439 , BMA G:503 , MAN G:507BINDING SITE FOR RESIDUE MAN G 506
07AC7SOFTWARESER C:30 , ASN C:92 , GLY G:441 , MAN G:506 , MAN G:508BINDING SITE FOR RESIDUE MAN G 507
08AC8SOFTWARECYS G:205 , LYS G:207 , ALA G:436 , MAN G:507BINDING SITE FOR RESIDUE MAN G 508
09AC9SOFTWARELYS G:117 , MAN G:504BINDING SITE FOR RESIDUE MAN G 509
10BC1SOFTWAREASN G:386 , THR G:388 , NAG G:511BINDING SITE FOR RESIDUE NAG G 510
11BC2SOFTWARENAG G:510BINDING SITE FOR RESIDUE NAG G 511
12BC3SOFTWAREASN G:229 , ASN G:241 , NAG G:513BINDING SITE FOR RESIDUE NAG G 512
13BC4SOFTWARENAG G:512 , BMA G:514BINDING SITE FOR RESIDUE NAG G 513
14BC5SOFTWARENAG G:513BINDING SITE FOR RESIDUE BMA G 514
15BC6SOFTWAREASN G:289 , GLN G:344 , NAG G:516BINDING SITE FOR RESIDUE NAG G 515
16BC7SOFTWAREGLN G:344 , NAG G:515BINDING SITE FOR RESIDUE NAG G 516
17BC8SOFTWAREHIS G:330 , ASN G:332 , THR G:415 , ARG G:444 , NAG G:518BINDING SITE FOR RESIDUE NAG G 517
18BC9SOFTWARENAG G:517BINDING SITE FOR RESIDUE NAG G 518
19CC1SOFTWARESER G:446 , ASN G:448 , NAG G:502 , NAG G:520BINDING SITE FOR RESIDUE NAG G 519
20CC2SOFTWARENAG G:519BINDING SITE FOR RESIDUE NAG G 520
21CC3SOFTWAREASN G:234 , THR G:236 , GLY G:237 , PRO G:238 , NAG G:522BINDING SITE FOR RESIDUE NAG G 521
22CC4SOFTWAREGLY G:237 , PRO G:238 , NAG G:521 , BMA G:523BINDING SITE FOR RESIDUE NAG G 522
23CC5SOFTWARENAG G:522BINDING SITE FOR RESIDUE BMA G 523
24CC6SOFTWAREVAL G:293 , ASN G:295 , ARG G:444 , MAN G:505BINDING SITE FOR RESIDUE NAG G 524
25CC7SOFTWAREASN G:276 , THR G:278 , NAG G:526BINDING SITE FOR RESIDUE NAG G 525
26CC8SOFTWARENAG G:525 , BMA G:527BINDING SITE FOR RESIDUE NAG G 526
27CC9SOFTWARENAG G:526BINDING SITE FOR RESIDUE BMA G 527

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1B:16 -B:84
2B:130 -B:159
3C:23 -C:88
4C:134 -C:194
5D:22 -D:92
6D:140 -D:196
7G:119 -G:205
8G:126 -G:196
9G:218 -G:247
10G:296 -G:331
11G:378 -G:445
12G:385 -G:418

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser C:7 -Pro C:8
2Trp C:94 -Pro C:95
3Tyr C:140 -Pro C:141
4Phe D:146 -Pro D:147
5Glu D:148 -Pro D:149
6Thr G:462 -Asn G:463

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RQS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RQS)

(-) Exons   (0, 0)

(no "Exon" information available for 4RQS)

(-) Sequences/Alignments

Asymmetric 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 B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eee...........eeee.....eeeeee..eeee........ee.hhhhhhhh...eee...hhhhheeeeeee..eeeeeeeeeeeeee....eee....eeeeee.......eeeee.....eeee...eee...hhhhheeeeeeeee..eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rqs B    1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQK  181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee........ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rqs C    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee......eeeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeee................ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rqs D    1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125||     141       151       161       171       181       191       201       211   
                                                                              52A                            82A||               100A|||||100J|                       126|                                                                                 
                                                                                                              82B|                100B|||||100K                        133                                                                                 
                                                                                                               82C                 100C||||||                                                                                                              
                                                                                                                                    100D|||||                                                                                                              
                                                                                                                                     100E||||                                                                                                              
                                                                                                                                      100F|||                                                                                                              
                                                                                                                                       100G||                                                                                                              
                                                                                                                                        100H|                                                                                                              
                                                                                                                                         100I                                                                                                              


Chain G from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...hhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee....................eeeeee.......eeee..eeee.............eee.........eee..........eeee....eeeeee...eeeehhhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhh.....eeeeeee..eee......eee..........eeeeeeeeeeee......eeeeee...hhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rqs G   86 LENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGAGHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGTNGTEIFRPGGGDMRDNWRSELYKYKVVKI  491
                                    95       105       115       125   ||  199       209       219       229       239       249       259       269       279       289       299||     338       348       358       368       378       388       414       424       434       444       454    || 466       476       486     
                                                                     129|                                                                                                       300|                                                               396|                                           459|                             
                                                                      194                                                                                                        330                                                                413                                            462
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  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 4RQS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RQS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RQS)

(-) Gene Ontology  (72, 76)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD4_HUMAN | P01730: 1cdh 1cdi 1cdj 1cdu 1cdy 1g9m 1g9n 1gc1 1jl4 1opn 1opt 1opw 1q68 1rzj 1rzk 1wbr 1wio 1wip 1wiq 2b4c 2jkr 2jkt 2klu 2nxy 2nxz 2ny0 2ny1 2ny2 2ny3 2ny4 2ny5 2ny6 2qad 3b71 3cd4 3j70 3jcb 3jcc 3jwd 3jwo 3lqa 3o2d 3s4s 3s5l 3t0e 4h8w 4jm2 4p9h 4q6i 4r2g 4r4h 5a7x 5a8h 5cay 5thr 5u1f 5vn3
        ENV_HV1Y2 | P35961: 1g9n 1rzk 1yyl 1yym 2i5y 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jo3 4jzw 4jzz 4k0a 4ka2 4laj 4r4f 4rwy 5a7x 5a8h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4RQS)