4J6R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC23 IN COMPLEX WITH HIV-1 GP120

Authors :   T. Zhou, S. Moquin, Kwong P. D.

Date :   11 Feb 13 (Deposition) - 08 May 13 (Release) - 29 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

Chains :   Asym./Biol. Unit : G,H,L

Keywords :   Hiv, Gp120, Cd4-Binding Site, Vrc23, Neutralization, Vaccine, Antibody, Envelope Protein, Immune System, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. S. Georgiev, N. A. Doria-Rose, T. Zhou, Y. D. Kwon, R. P. Staupe, S. Moquin, G. Y. Chuang, M. K. Louder, S. D. Schmidt, H. R. Altae-Tran, R. T. Bailer, K. Mckee, M. Nason, S. O'Dell, G. Ofek, M. Pancera, S. Srivatsan, L. Shapiro, M. Connors, S. A. Migueles, L. Morris, Y. Nishimura, M. A. Martin, J. R. Mascola, P. D. Kwong
Delineating Antibody Recognition In Polyclonal Sera From Patterns Of Hiv-1 Isolate Neutralization.
Science V. 340 751 2013
PubMed-ID: 23661761 | Reference-DOI: 10.1126/SCIENCE.1233989

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
	Chains	:	G
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	293F
	Expression System Plasmid	:	PVRC8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC23
	Chains	:	H
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	293F
	Expression System Plasmid	:	PVRC8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - LIGHT CHAIN OF ANTIBODY VRC23
	Chains	:	L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	293F
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric/Biological Unit	:	G	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 30)

No.	Name	Count	Type	Full Name
1	BU3	1	Ligand/Ion	(R,R)-2,3-BUTANEDIOL
2	CA	2	Ligand/Ion	CALCIUM ION
3	EDO	15	Ligand/Ion	1,2-ETHANEDIOL
4	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
5	NAG	9	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
7	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (29, 29)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE G:233 , ASN G:234 , THR G:236 , LEU G:238 , HOH G:718 , HOH G:820	BINDING SITE FOR RESIDUE NAG G 501
02	AC2	SOFTWARE	ASP G:230 , GLU G:231 , ASN G:241	BINDING SITE FOR RESIDUE NAG G 502
03	AC3	SOFTWARE	GLU G:211 , PRO G:212 , ASN G:262 , GLU G:446 , SER G:447 , HOH G:619 , HOH G:658 , HOH G:738 , HOH G:799	BINDING SITE FOR RESIDUE NAG G 503
04	AC4	SOFTWARE	ASN G:276 , THR G:278 , VAL L:29 , GLY L:30 , ASP L:32 , GLN L:90 , TYR L:91 , HOH L:513	BINDING SITE FOR RESIDUE NAG G 504
05	AC5	SOFTWARE	LYS G:295 , HIS G:330 , ASN G:332 , HOH G:828 , HOH G:835 , HOH G:881	BINDING SITE FOR RESIDUE NAG G 505
06	AC6	SOFTWARE	LYS G:117 , ASN G:363 , THR G:372 , ASN G:386 , SER G:388 , NAG G:507 , HOH G:687 , HOH G:782 , HOH G:797 , HOH G:832 , HOH G:909	BINDING SITE FOR RESIDUE NAG G 506
07	AC7	SOFTWARE	LYS G:117 , ASN G:386 , SER G:388 , NAG G:506 , HOH G:676 , HOH G:677 , HOH G:743 , HOH G:782	BINDING SITE FOR RESIDUE NAG G 507
08	AC8	SOFTWARE	ASN G:392 , HOH G:740	BINDING SITE FOR RESIDUE NAG G 508
09	AC9	SOFTWARE	LEU G:265 , PRO G:291 , GLU G:446 , ASN G:448 , HOH G:683	BINDING SITE FOR RESIDUE NAG G 509
10	BC1	SOFTWARE	LYS G:421 , GLN G:422 , ILE G:423	BINDING SITE FOR RESIDUE CA G 510
11	BC2	SOFTWARE	ASN G:234 , ILE G:272 , ARG G:273 , SER G:274 , TYR G:352 , HOH G:667 , HOH G:724 , HOH G:918	BINDING SITE FOR RESIDUE EDO G 511
12	BC3	SOFTWARE	GLY G:250 , LYS G:252 , ASN G:262 , GLY G:263 , HOH G:672 , HOH G:826	BINDING SITE FOR RESIDUE EDO G 512
13	BC4	SOFTWARE	VAL G:254 , LEU G:261 , GLY G:263 , ASN G:478 , HOH G:613 , HOH G:645 , HOH G:672	BINDING SITE FOR RESIDUE EDO G 513
14	BC5	SOFTWARE	THR G:400 , ASP G:403	BINDING SITE FOR RESIDUE EDO G 514
15	BC6	SOFTWARE	GLU H:23 , THR H:75 , HOH H:462 , HOH H:505	BINDING SITE FOR RESIDUE MPD H 301
16	BC7	SOFTWARE	SER H:7 , ARG H:19 , SER H:21	BINDING SITE FOR RESIDUE EDO H 302
17	BC8	SOFTWARE	GLU H:148 , PRO H:149 , VAL H:150 , ALA H:168 , HOH H:621	BINDING SITE FOR RESIDUE EDO H 303
18	BC9	SOFTWARE	TYR H:32 , ARG H:94 , VAL H:96 , PHE H:102 , HOH H:616	BINDING SITE FOR RESIDUE EDO H 304
19	CC1	SOFTWARE	ALA H:9 , PRO H:149 , HOH H:481 , HOH H:594 , HOH H:725	BINDING SITE FOR RESIDUE EDO H 305
20	CC2	SOFTWARE	LEU H:141 , VAL H:169 , SER H:177 , LEU H:178 , SER H:179 , HOH H:420 , THR L:178 , HOH L:412 , HOH L:413	BINDING SITE FOR RESIDUE EDO H 306
21	CC3	SOFTWARE	LYS H:13 , ALA H:114 , SER H:115 , THR H:116 , HOH H:426 , HOH H:655	BINDING SITE FOR RESIDUE EDO H 307
22	CC4	SOFTWARE	THR H:151 , SER H:153 , ASN H:197 , HOH H:658 , HOH H:679	BINDING SITE FOR RESIDUE EDO H 308
23	CC5	SOFTWARE	GLN H:105 , GLY H:106 , HOH H:617 , HOH H:654 , HOH H:681 , HOH H:717	BINDING SITE FOR RESIDUE EDO H 309
24	CC6	SOFTWARE	SER H:161 , GLY H:162 , HOH H:456 , HOH H:592 , HOH H:732 , SER L:65 , GLY L:66 , ASP L:167 , ASP L:170 , HOH L:453	BINDING SITE FOR RESIDUE TRS H 310
25	CC7	SOFTWARE	ARG L:15 , HIS L:68 , HOH L:540 , HOH L:743	BINDING SITE FOR RESIDUE CA L 301
26	CC8	SOFTWARE	ARG H:44 , MET L:4 , GLN L:100 , HOH L:415	BINDING SITE FOR RESIDUE EDO L 302
27	CC9	SOFTWARE	LYS L:39 , PRO L:80 , GLU L:81 , VAL L:83 , HOH L:583 , HOH L:629	BINDING SITE FOR RESIDUE EDO L 303
28	DC1	SOFTWARE	LYS L:107 , BU3 L:305 , HOH L:582	BINDING SITE FOR RESIDUE EDO L 304
29	DC2	SOFTWARE	ARG L:108 , THR L:109 , EDO L:304 , HOH L:537	BINDING SITE FOR RESIDUE BU3 L 305

Asymmetric/Biological Unit

No.	Residues
1	G:54	-	G:74
2	G:119	-	G:205
3	G:218	-	G:247
4	G:228	-	G:239
5	G:296	-	G:331
6	G:378	-	G:445
7	G:385	-	G:418
8	H:22	-	H:92
9	H:140	-	H:196
10	L:23	-	L:88
11	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Ser L:7	-	Pro L:8
4	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 4J6R)

(no "PROSITE Motif" information available for 4J6R)

(no "Exon" information available for 4J6R)

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 G from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhheee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..eeee......hhhhhheeeee..eeeee.......eee...........eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee...hhhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j6r G   44 VWRDADTTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLDNVTEKFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTGGSAITQACPKVSFEPIPIHYCTPAGFAILKCKDEGFNGTGLCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKNITIRSENITNNAKIIIVQLVQPVTIKCIRDIRQAHCNVTRSRWNKTLQEVAEKLRTYFGNKTIIFANSSGGDLEITTHSFNCGGEFFYCNTSGLFNSTWYVNSTWNDTNDTITLPCRIKQIINMWQRAGQAMYAPPIPGVIKCESNITGLLLTRDGGKDNNVNETFRPGGGDMRDNWRSELYKYKVVEIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296 ||    332       342       352    || 363       373       383       393       403||     419       429       439       449       459       469       479       489   
                                                                                                          124|                                                                                                 298|                             357|                                          404|                                                                                 
                                                                                                           198                                                                                                  325                              359                                           411

Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee..eeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4j6r H    1 xVQFVQSGAEVKKPGASVRVSCEASGYSFTDYVLQWIRQAPGQRPEWMGWIKPERGAVSYAPQFQGRLTLTRDLYTETAYMHFKNLRSDDTAIYYCARGVRRDASWWLQFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212  
                            1-PCA                                             52A                            82A||               100A|||                                                                                                                  
                                                                                                              82B|                100B||                                                                                                                  
                                                                                                               82C                 100C|                                                                                                                  
                                                                                                                                    100D

Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d4j6rl1 L:1-107 automated matches                                                                      d4j6rl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4j6r L    1 EIVMTQSPVTVSVSRGGTATLSCRASQGVGSDVAWYQHKPGQTPRLLIYGASTRASGVPERFSGSGFHVDFTLSISGLQPEDVAIYYCQQYETFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90||     104       114       124       134       144       154       164       174       184       194       204       214
                                                                                                                     91|                                                                                                                      
                                                                                                                      96

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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

d4j6rl1

L:1-107

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

d4j6rl2

L:108-214

(no "CATH Domain" information available for 4J6R)

(no "Pfam Domain" information available for 4J6R)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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3se8	VRC03
3se9	VRC-PG04
3u7y	NIH45-46
4jb9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 30)

Sites (29, 29)

SS Bonds (11, 11)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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