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Title :   CRYSTAL STRUCTURE OF NON-NEUTRALIZING AND ADCC-POTENT ANTIBODY N5-I5 IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND SCD4.

Authors :   W. D. Tolbert, P. Acharya, P. D. Kwong, M. Pazgier

Date :   24 Sep 12 (Deposition) - 09 Apr 14 (Release) - 22 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Hiv-1 Gp120, Clade A/E 93Th057, Viral Protein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Acharya, W. D. Tolbert, N. Gohain, X. Wu, L. Yu, T. Liu, W. Huang, C. C. Huang, Y. D. Kwon, R. K. Louder, T. S. Luongo, J. S. Mclellan, M. Pancera, Y. Yang, B. Zhang, R. Flinko, J. S. Foulke, M. M. Sajadi, R. Kamin-Lewis, J. E. Robinson, L. Martin, P. D. Kwong, Y. Guan, A. L. Devico, G. K. Lewis, M. Pazgier
Structural Definition Of An Antibody-Dependent Cellular Cytotoxicity Response Implicated In Reduced Risk For Hiv-1 Infection.
J. Virol. V. 88 12895 2014
PubMed-ID: 25165110 | Reference-DOI: 10.1128/JVI.02194-14

Molecule 1 - HIV-1 CLADE A/E 93TH057 (H375S) GP120
	Chains	:	G
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293 GNT1-
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB HEAVY CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5
	Chains	:	H
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FAB LIGHT CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5
	Chains	:	L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - T-CELL SURFACE GLYCOPROTEIN CD4
	Chains	:	C
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293
	Expression System Taxid	:	9606
	Gene	:	CD4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	T-CELL SURFACE ANTIGEN T4/LEU-3

		1	2	3	4
Asymmetric/Biological Unit	:	C	G	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MRD	3	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU G:87 , ASN G:88 , GLY G:198 , LYS L:150 , SER L:153	BINDING SITE FOR RESIDUE NAG G 501
02	AC2	SOFTWARE	ASN G:234 , THR G:236 , ILE G:272 , HIS G:352 , HOH G:801	BINDING SITE FOR RESIDUE NAG G 502
03	AC3	SOFTWARE	ASN G:229 , ASN G:241 , HOH G:915	BINDING SITE FOR RESIDUE NAG G 503
04	AC4	SOFTWARE	LYS G:252 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:661 , HOH G:673 , HOH G:744 , HOH G:758	BINDING SITE FOR RESIDUE NAG G 504
05	AC5	SOFTWARE	LYS C:90 , ASN G:276 , THR G:278 , ASN G:279 , HOH G:630 , HOH G:800	BINDING SITE FOR RESIDUE NAG G 505
06	AC6	SOFTWARE	GLU G:269 , ILE G:270 , ASN G:289 , LYS G:348 , HOH G:780	BINDING SITE FOR RESIDUE NAG G 506
07	AC7	SOFTWARE	ASN G:295 , GLU G:332 , LYS G:442 , HOH G:711 , HOH G:888	BINDING SITE FOR RESIDUE NAG G 507
08	AC8	SOFTWARE	ASN G:334 , LYS G:337	BINDING SITE FOR RESIDUE NAG G 508
09	AC9	SOFTWARE	THR G:372 , ASN G:386 , THR G:388 , HOH G:683 , HOH G:900	BINDING SITE FOR RESIDUE NAG G 509
10	BC1	SOFTWARE	GLN G:389 , ASN G:392 , CYS G:395 , CYS G:410	BINDING SITE FOR RESIDUE NAG G 510
11	BC2	SOFTWARE	VAL G:224 , SER G:244 , ILE G:491	BINDING SITE FOR RESIDUE MRD G 511
12	BC3	SOFTWARE	VAL G:255 , SER G:375 , PHE G:376 , PHE G:382 , ILE G:424 , ASN G:425 , MET G:426 , TRP G:427 , HOH G:632 , HOH G:814 , HOH G:889	BINDING SITE FOR RESIDUE MRD G 512
13	BC4	SOFTWARE	GLY H:42 , LYS H:43 , TYR L:87 , GLY L:100 , GLY L:101	BINDING SITE FOR RESIDUE MRD L 301
14	BC5	SOFTWARE	HOH C:402 , LEU G:122 , GLN G:432 , HOH G:913	BINDING SITE FOR RESIDUE GOL C 201

Asymmetric/Biological Unit

No.	Residues
1	C:16	-	C:84
2	C:130	-	C:159
3	G:54	-	G:74
4	G:119	-	G:205
5	G:218	-	G:247
6	G:228	-	G:239
7	G:296	-	G:331
8	G:378	-	G:445
9	G:385	-	G:418
10	G:395	-	G:410
11	H:22	-	H:92
12	H:140	-	H:196
13	L:23	-	L:88
14	L:135	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Tyr L:141	-	Pro L:142

(no "SAP(SNP)/Variant" information available for 4H8W)

(no "PROSITE Motif" information available for 4H8W)

(no "Exon" information available for 4H8W)

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 C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                 
               SCOP domains d4h8wc1 C:1-97 CD4 V-set domains                                                                 d4h8wc2 C:98-176 CD4 C2-set domains                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eee...........eeeee....eeeeee..eeee....hhh.ee.hhhhhhhh...eee...hhhhheeeeeee..eeeeeeeeeeeeee...........eeeeee.......eeeee.....eee...eeee...hhhhheeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4h8w C    1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVV  176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain G from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhhhhee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee............eeee....eeeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh........eeeeeeeee.eee......eee........eeeeeeeeeeeeee.....eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4h8w G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCICNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348      |359       369       379       389      |412       422       432       442       452      |465       475       485       
                                                                                                          124|                                                                                                    301|                            355|                                    396|                                              459|                             
                                                                                                           198                                                                                                     324                             357                                     410                                               463

Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee.....eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee.hhhhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4h8w H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSTYAMSWVRQAPGKGLEWVSSINNSGRNTFSADSVKGRFTISRDNSKNTLFLVMNSLRAEDTAVYYCAKDLRLGGGSDYWGQGTLVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124  ||   141       151       161       171       181       191       201       211  
                                                                              52A                            82A||               100A|                        127|                                                                              
                                                                                                              82B|                100B                         135                                                                              
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d4h8wl1 L:3-108 automated matches                                                                              d4h8wl2 L:109-209 automated matches                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeehhhhhheee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4h8w L    3 SALTQPASVSGSPGQSITISCTGTSSDVGSYNFVSWYQQHPGKAPKLMIYEVSERPSGISNRFSGSKSGNTASLTISGLQAEDEADYYCSSYAGSTTFRVFGGGTKLTVRGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  209
                                    12        22     |||29        39        49        59        69        79        89      ||97       107       117       127       137       147       157       167       177       187       197       207  
                                                   27A||                                                                  95A|                                                                                                                  
                                                    27B|                                                                   95B                                                                                                                  
                                                     27C

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "CATH Domain" information available for 4H8W)

(no "Pfam Domain" information available for 4H8W)

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 ]
		Tyr L:141 - Pro L:142	[ RasMol ]

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1g9m	T-CELL SURFACE GLYCOPROTEIN CD4
3tgt	HIV-1 CLADE A/E 93TH057 GP120
3tnn	FAB OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (14, 14)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 4)

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Gene Ontology (66, 69)

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