4RWY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF VH1-46 GERMLINE-DERIVED CD4-BINDING SITE-DIRECTED ANTIBODY 8ANC131 IN COMPLEX WITH HIV-1 CLADE B YU2 GP120

Authors :   P. Acharya, T. S. Luongo, P. D. Kwong

Date :   08 Dec 14 (Deposition) - 01 Jul 15 (Release) - 01 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

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

Keywords :   Hiv-1 Attachment Protein, Broadly Neutralizing Antibody 8Anc131, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Zhou, R. M. Lynch, L. Chen, P. Acharya, X. Wu, N. A. Doria-Rose, M. G. Joyce, D. Lingwood, C. Soto, R. T. Bailer, M. J. Ernandes, R. Kong, N. S. Longo, M. K. Louder, K. Mckee, S. O'Dell, S. D. Schmidt, L. Tran, Z. Yang, A. Druz, T. S. Luongo, S. Moquin, S. Srivatsan, Y. Yang, B. Zhang, A. Zheng, M. Pancera, T. Kirys, I. S. Georgiev, T. Gindin, H. P. Peng, A. S. Yang, J. C. Mullikin, M. D. Gray, L. Stamatatos, D. R. Burton, W. C. Koff, M. S. Cohen, B. F. Haynes, J. P. Casazza, M. Connors, D. Corti, A. Lanzavecchia, Q. J. Sattentau, R. A. Weiss, A. P. West, P. J. Bjorkman, J. F. Scheid, M. C. Nussenzweig, L. Shapiro, J. R. Mascola, P. D. Kwong
Structural Repertoire Of Hiv-1-Neutralizing Antibodies Targeting The Cd4 Supersite In 14 Donors.
Cell(Cambridge, Mass. ) V. 161 1280 2015
PubMed-ID: 26004070 | Reference-DOI: 10.1016/J.CELL.2015.05.007

Molecule 1 - HIV-1 YU2 GP120
	Chains	:	A
	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 Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	CLADE B YU2

Molecule 2 - ANTIBODY 8ANC131 HEAVY CHAIN
	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 Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - ANTIBODY 8ANC131 LIGHT CHAIN
	Chains	:	L
	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 Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric/Biological Unit	:	A	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 13)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	NA	1	Ligand/Ion	SODIUM ION
4	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:52 , GLN A:103 , GLU A:106 , ASP A:107 , TYR A:217 , ARG A:327 , ILE A:420 , LYS A:421 , GLN A:422 , ILE A:423 , HOH A:606	BINDING SITE FOR RESIDUE EPE A 507
02	AC2	SOFTWARE	GLU A:47 , PHE A:93 , ASN A:94 , LYS A:97 , LYS A:487 , HOH A:650	BINDING SITE FOR RESIDUE EDO A 508
03	AC3	SOFTWARE	HOH H:475	BINDING SITE FOR RESIDUE EDO H 301
04	AC4	SOFTWARE	VAL H:150 , THR H:165 , HOH H:419 , HOH H:465	BINDING SITE FOR RESIDUE EDO H 302
05	AC5	SOFTWARE	THR H:28 , PHE H:29 , PHE H:32 , ILE H:34 , ILE H:51 , LYS H:52 , ARG H:71	BINDING SITE FOR RESIDUE EDO H 303
06	AC6	SOFTWARE	THR H:19	BINDING SITE FOR RESIDUE EDO H 304
07	AC7	SOFTWARE	ASN A:234 , THR A:236 , PRO A:238 , NAG A:501	BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 234
08	AC8	SOFTWARE	GLU A:211 , PRO A:212 , VAL A:254 , LEU A:261 , ASN A:262 , SER A:446 , SER A:447 , HOH A:614 , HOH A:618	BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 262
09	AC9	SOFTWARE	ASN A:276 , THR A:278 , NAG A:502 , HOH A:672 , HOH A:677 , ASN L:31	BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 276
10	BC1	SOFTWARE	GLU A:267 , GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , GLN A:344 , LYS A:348	BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 289
11	BC2	SOFTWARE	ASN A:295 , ASN A:332 , LEU A:333 , ARG A:444	BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 295
12	BC3	SOFTWARE	VAL A:372 , ASN A:386 , THR A:388	BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 386

Asymmetric/Biological Unit

No.	Residues
1	A:54	-	A:74
2	A:119	-	A:205
3	A:218	-	A:247
4	A:228	-	A:239
5	A:296	-	A:331
6	A:378	-	A:445
7	A:385	-	A:418
8	H:22	-	H:92
9	H:140	-	H:196
10	H:216	-	L:214
11	L:23	-	L:88
12	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Thr A:257	-	Gln A:258
2	Gln H:1	-	Gly H:2
3	Ala H:100A	-	Pro H:100B
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Ser L:7	-	Pro L:8
7	Pro L:51	-	Ser L:52
8	Thr L:94	-	Pro L:95
9	Tyr L:140	-	Pro L:141

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

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

(no "Exon" information available for 4RWY)

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:337
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee........hhhhhhhhhhee.......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee...........eeeeeeee..ee.......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwy A   44 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 329       339       349       359       369       379       389    || 415       425       435       445       455       465       475       485       
                                                                                                          124|                                                                                                    301|                                                                  394|                                                                                 
                                                                                                           198                                                                                                     325                                                                   411

Chain H from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.eee.....eeeeeeehhhhhhhheeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee..............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwy H    1 QGQLVQSGGGLKKPGTSVTISCLASEYTFNEFVIHWIRQAPGQGPLWLGLIKRSGRLMTAYNFQDRLSLRRDRSTGTVFMELRGLRPDDTAVYYCARDGLGEVAPDYRYGIDVWGQGSTVIVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC  216
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G|      109       119       129       139       149       159       169       179       189       199       209       
                                                                                                            82A||               100A|||||||                                                                                                                    
                                                                                                             82B|                100B||||||                                                                                                                    
                                                                                                              82C                 100C|||||                                                                                                                    
                                                                                                                                   100D||||                                                                                                                    
                                                                                                                                    100E|||                                                                                                                    
                                                                                                                                     100F||                                                                                                                    
                                                                                                                                      100G|                                                                                                                    
                                                                                                                                       100H

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee...eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeee............eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwy L    1 EIVLTQSPATLSLSPGERATLSCRASQGLNFVVWYQQKRGQAPRLLIHAPSGRAPGVPDRFSARGSGTEFSLVISSVEPDDFAIYYCQEYSSTPYNFGPGTRVDRKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC  214
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
                                                     27|                                                                                                                                                                                         
                                                      29

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 '\|'

(no "SCOP Domain" information available for 4RWY)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala H:100A - Pro H:100B	[ RasMol ]
		Gln H:1 - Gly H:2	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Pro L:51 - Ser L:52	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Thr A:257 - Gln A:258	[ RasMol ]
		Thr L:94 - Pro L:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	4rwy
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (12, 12)

SS Bonds (12, 12)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (21, 21)

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