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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 ENVELOPE TRIMER 16055 NFL TD CC (T569G) IN COMPLEX WITH FABS 35022 AND PGT124
 
Authors :  F. Garces, R. L. Stanfield, I. A. Wilson
Date :  26 Jan 17  (Deposition) - 24 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.94
Chains :  Asym./Biol. Unit :  B,D,E,G,H,L
Keywords :  Hiv-1 Antibody Glycoprotein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Guenaga, F. Garces, N. De Val, R. L. Stanfield, V. Dubrovskaya, B. Higgins, B. Carrette, A. B. Ward, I. A. Wilson, R. T. Wyatt
Glycine Substitution At Helix-To-Coil Transitions Facilitates The Structural Determination Of A Stabilized Subtype C Hiv Envelope Glycoprotein.
Immunity V. 46 792 2017
PubMed-ID: 28514686  |  Reference-DOI: 10.1016/J.IMMUNI.2017.04.014

(-) Compounds

Molecule 1 - GLYCOPROTEIN GP120
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293S FREESTYLE
    Expression System Taxid: 9606
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 16055
 
Molecule 2 - GLYCOPROTEIN GP41
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293S FREESTYLE
    Expression System Taxid: 9606
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 16055
 
Molecule 3 - FAB PGT124 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - FAB PGT124 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - FAB 35022 HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 6 - FAB 35022 LIGHT CHAIN
    Chains: E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : BDEGHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 56)

Asymmetric/Biological Unit (3, 56)
No.NameCountTypeFull Name
1BMA5Ligand/IonBETA-D-MANNOSE
2MAN16Ligand/IonALPHA-D-MANNOSE
3NAG35Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:611 , SER B:613 , LEU B:645binding site for Mono-Saccharide NAG B 702 bound to ASN B 611
02AC2SOFTWARELYS B:617 , ASN B:625 , MET B:626 , GLU D:1 , TYR D:32 , LYS D:94 , GLY D:95 , LEU D:96 , TYR D:101binding site for Mono-Saccharide NAG B 703 bound to ASN B 625
03AC3SOFTWAREARG B:633 , ASN B:637binding site for Mono-Saccharide NAG B 701 bound to ASN B 637
04AC4SOFTWARESER B:528 , ASN D:30 , PHE D:31 , HIS D:33 , SER D:52 , SER D:54 , ASP D:56 , ASN D:58 , ARG D:98 , ASP D:99 , GLY D:100 , SER D:100A , THR D:100C , HIS E:95 , ASN E:96 , ASN G:88binding site for Poly-Saccharide residues NAG G 738 through MAN G 744 bound to ASN G 88
05AC5SOFTWAREASN G:135 , ASN G:156 , SER G:158 , TYR G:173 , ARG L:94binding site for Poly-Saccharide residues NAG G 715 through MAN G 719 bound to ASN G 156
06AC6SOFTWARETHR G:128 , GLU G:130 , ASN G:160binding site for Mono-Saccharide NAG G 707 bound to ASN G 160
07AC7SOFTWAREARG G:192 , ILE G:194 , ASN G:197 , THR G:198binding site for Poly-Saccharide residues NAG G 713 through NAG G 714 bound to ASN G 197
08AC8SOFTWAREASN G:230 , THR G:232 , PHE G:233 , PRO G:238 , CYS G:239 , NAG G:711binding site for Poly-Saccharide residues NAG G 720 through NAG G 721 bound to ASN G 230
09AC9SOFTWAREVAL D:72E , ASN G:234 , SER G:274 , NAG G:721binding site for Poly-Saccharide residues NAG G 711 through NAG G 712 bound to ASN G 234
10AD1SOFTWAREGLU G:83 , ASN G:229 , ASN G:241binding site for Poly-Saccharide residues NAG G 722 through BMA G 724 bound to ASN G 241
11AD2SOFTWAREGLU G:64 , PRO G:212 , LEU G:261 , ASN G:262 , ARG G:379 , LYS G:446 , SER G:447 , NAG G:705binding site for Poly-Saccharide residues NAG G 745 through MAN G 750 bound to ASN G 262
12AD3SOFTWAREASN G:276 , THR G:278 , ASN G:279binding site for Mono-Saccharide NAG G 708 bound to ASN G 276
13AD4SOFTWAREGLY G:268 , ILE G:270 , ASN G:289binding site for Mono-Saccharide NAG G 700 bound to ASN G 289
14AD5SOFTWAREASN G:301 , THR G:303 , ILE G:323binding site for Poly-Saccharide residues NAG G 751 through NAG G 752 bound to ASN G 301
15AD6SOFTWARETYR G:330 , ASN G:332 , THR G:415 , ARG H:100 , GLY H:100C , VAL H:100E , SER L:30 , ASN L:50 , ASN L:51 , GLN L:52 , PRO L:66 , ASP L:67 , ILE L:67Abinding site for Poly-Saccharide residues NAG G 728 through MAN G 737 bound to ASN G 332
16AD7SOFTWAREASN G:360 , THR G:394 , THR G:465binding site for Poly-Saccharide residues NAG G 725 through NAG G 726 bound to ASN G 360
17AD8SOFTWAREASN G:386 , SER G:388 , NAG G:701binding site for Poly-Saccharide residues NAG G 709 through NAG G 710 bound to ASN G 386
18AD9SOFTWAREASN G:392 , NAG G:710binding site for Poly-Saccharide residues NAG G 701 through NAG G 702 bound to ASN G 392
19AE1SOFTWAREASN G:398binding site for Mono-Saccharide NAG G 704 bound to ASN G 398
20AE2SOFTWAREASN G:442 , THR G:444binding site for Mono-Saccharide NAG G 703 bound to ASN G 442
21AE3SOFTWAREASN G:448 , NAG G:745binding site for Poly-Saccharide residues NAG G 705 through NAG G 706 bound to ASN G 448
22AE4SOFTWAREPRO G:354 , SER G:462 , ASN G:463binding site for Mono-Saccharide NAG G 727 bound to ASN G 463

(-) SS Bonds  (20, 20)

Asymmetric/Biological Unit
No.Residues
1B:598 -B:604
2D:22 -D:92
3D:140 -D:196
4E:22 -E:90
5E:91 -E:99
6E:138 -E:197
7G:54 -G:74
8G:119 -G:205
9G:126 -G:196
10G:131 -G:157
11G:201 -G:433
12G:218 -G:247
13G:228 -G:239
14G:296 -G:331
15G:378 -G:445
16G:385 -G:418
17H:22 -H:92
18H:138 -H:194
19L:23 -L:88
20L:135 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Tyr L:141 -Pro L:142
2Phe H:144 -Pro H:145
3Glu H:146 -Pro H:147
4Phe D:146 -Pro D:147
5Glu D:148 -Pro D:149
6Ala E:131 -Asn E:132
7Tyr E:144 -Pro E:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UM8)

(-) Exons   (0, 0)

(no "Exon" information available for 5UM8)

(-) 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 B from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh..hhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.................hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5um8 B  521 GFLGAAGSTMGAASITLTVQARQLLSGIVQQQLQLGVWGIKQLQTRVLAIERYLKDQQLLGIWGCSGKLICTTAVPWNSSWSNKSHDEIWGNMTWMQWDREISNYTNTIYRLLEDSQNQQEQNEKDLLA  662
                                   530       540       550 ||    573       583       593       603       613       623       633       643       653         
                                                         552|                                                                                                
                                                          566                                                                                                


Chain D from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeee...ee.....ee.eeeeee...hhhhheeeeeeee..........eeee...eeeee........eeeeeeeeeee....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.........eeeeee....eeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5um8 D    1 EGQLVQSGAELKKPGASVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNLAPAFQDRVIMTTDTEVPVTSFTSTGAAYMEIRNLKFDDTGTYFCAKGLLRDGSSTWLPYLWGQGTLLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGLEV  222
                                    10        20        30        40        50  |     59        69   ||||72G|       81 |||    88        98  |||||102       112       122       132       142       152       162       172       182       192       202       212       222
                                                                              52A                  72A|||||||        82A||               100A|||||                                                                                                                          
                                                                                                    72B||||||         82B|                100B||||                                                                                                                          
                                                                                                     72C|||||          82C                 100C|||                                                                                                                          
                                                                                                      72D||||                               100D||                                                                                                                          
                                                                                                       72E|||                                100E|                                                                                                                          
                                                                                                        72F||                                 100F                                                                                                                          
                                                                                                         72G|                                                                                                                                                               
                                                                                                          72H                                                                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeee.....eeeee..........eeeeee.......eeee.............eeeee...eeeeee...hhhhh.eeeeeee......ee...eeeeee.......eeeee....hhhhh..eeeeeeeeee.....eeeeee...ee...eee...ee.....eeeeeeeeehhhhhh....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5um8 E    2 SVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPGISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQSKANPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   


Chain G from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....ee......eee...........................eeee....eeee...hhhhhhhhhhhhhhhhhhh.............eeee..............eeeeeeeee......eeeeeeeee...eeeee........eeee......................eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeeeeeee.eeeee.....eeeee..........eeeehhhhhhhhhhhhhhhhhhhh....eee............eeeee..eeeee........ee..............eeeeeeee.ee.........ee.....eeeeeeeeeeeeeeee.........eeeee.....hhhhhhhhh..eeeee..eeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5um8 G   32 GNLWVTVYYGVPVWKDAETTLFCASDAKAYEKEKHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVEQMHTDVISLWDQSLKPCVKLTPLCVTLECRQVNTTNATNVTNGEEIKNCSFNATTELRDKKQKVYALFYRLDIVPLEEERKGNSSKYRLINCNTSACTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENLTNNVKTIIVHLNESVEIVCTRPNNNTRKSIRIGPGQTFYATGDIIGNIRQAYCNISKDDWIRTLQRVGKKLAEHFPRRIINFTSPAGGDLEITTHSFNCRGEFFYCNTSSLFNSTYNPNDTNSSSNSSLDITIPCRIKQIINMWQRVGQCMYAPPIEGNITCKSNITGLLLVRDGGVESNETEIFRPGGGDMRNNWRSELYKYKVVEIKPLGIAPTRAKRRVVEGGG  510
                                    41        51        61        71        81        91       101       111       121       131       147       157       167       177      186A|||    193       203       213       223       233       243       253       263       273       283       293       303     ||315      |324       334       344       354|      365       375       385       395      |409       419       429       439       449       459       469       479       489       499       509 
                                                                                                                                      140|                                    186A|||                                                                                                                        309|      321A                              354|                                           402|                                                                                                       
                                                                                                                                       147                                     186B||                                                                                                                         312                                         356                                            407                                                                                                       
                                                                                                                                                                                186C|                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                 186D                                                                                                                                                                                                                                                                                                                              


Chain H from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee...hhhhheeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeeeee........eeeeeeeeee...eeeee........eeeee..........eeeeeeeeee.....eeee........eee...eee...eeeeeeeeee..........eeeeehhhhh...eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5um8 H    1 QVQLQESGPGLVRPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYNPSLNSRAVISRDTSKNQLSLQLRSVTTADTAIYFCATARRGQRIYGVVSFGEFFYYYYMDVWGKGTAVTVSSASTKGPSVFPLAPSSSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  214
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G||||||100Q|      109       119      |130       140       150       160       170       180       190       200       210    
                                                                                                            82A||               100A|||||100J||||||||                       126|                                                                                      
                                                                                                             82B|                100B|||||100K|||||||                        128                                                                                      
                                                                                                              82C                 100C|||||100L||||||                                                                                                                 
                                                                                                                                   100D|||||100M|||||                                                                                                                 
                                                                                                                                    100E|||| 100N||||                                                                                                                 
                                                                                                                                     100F|||  100O|||                                                                                                                 
                                                                                                                                      100G||   100P||                                                                                                                 
                                                                                                                                       100H|    100Q|                                                                                                                 
                                                                                                                                        100I     100R                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eee............eeeee......eeee.............eee...........eee...hhhhh.eeeee...............eeeeee.......eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5um8 L    6 SYVSPLSVALGETARISCGRQALGSRAVQWYQHKPGQAPILLIYNNQDRPSGIPERFSGTPDINFGTTATLTISGVEVGDEADYYCHMWDSRSGFSWSFGGATRLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  210
                                    15        25        35        45        55        65  |||   72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209 
                                                                                        67A||                          95A||                                                                                                                   
                                                                                         67B|                           95B|                                                                                                                   
                                                                                          67C                            95C
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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 '|'

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(no "SCOP Domain" information available for 5UM8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UM8)

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(no "Pfam Domain" information available for 5UM8)

(-) Gene Ontology  (0, 0)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5UM8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5UM8)