1RZJ: HIV-1 HXBC2 GP120 envelope glycoprotein

HIV-1 HXBC2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing antibody 17B. Determined by X-ray diffraction at 2.2 Å resolution. Released 3 Feb 2004.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 4
Atoms: 7,947
Mol. weight: 107.24 kDa
Ligands: NAG, IPA
Released: 3 Feb 2004

Explore 1RZJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RZJ contains 30 α-helices and 90 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	12-14	3	8
β-strand	17	1	9
β-strand	26-30	5	7
β-strand	35-40	6	7
β-strand	43-46	4	7
α-helix	52-54	3
β-strand	55-56	2	8
α-helix	62-64	3
β-strand	66	1	9
β-strand	69-71	3	8
β-strand	80-86	7	7
β-strand	89-98	10	7
β-strand	99-102	4	10
β-strand	108-109	2	11
β-strand	114-119	6	10
α-helix	126	1
β-strand	127-131	5	12
β-strand	137-140	4	12
β-strand	143-146	4	10
α-helix	151-153	3
β-strand	155-163	9	12
β-strand	166-174	9	12
β-strand	176-177	2	11

Chain G: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	84-93	10	1
α-helix	95-97	3
α-helix	99-113	15
β-strand	120-123	4	2
β-strand	199-202	4	2
α-helix	212-214	3
β-strand	215	1	3
β-strand	218	1	4
α-helix	219-220	2
β-strand	223-228	6	1
β-strand	237-245	9	1
β-strand	247	1	4
α-helix	248-250	3
β-strand	251	1	3
β-strand	256	1	5
β-strand	259-261	3	6
β-strand	271-273	3	6
β-strand	284-297	14	6
β-strand	330-334	5	6
α-helix	335-352	18
β-strand	358-361	4	6
β-strand	367	1	7
α-helix	369-372	4
β-strand	374-378	5	5
β-strand	381-385	5	5
α-helix	388-390	3
β-strand	393-395	3	6
β-strand	413-417	5	6
β-strand	420-421	2	5
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	436-438	3
β-strand	444-456	13	6
β-strand	465-470	6	6
α-helix	475-483	9
β-strand	486-490	5	1

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
α-helix	7-9	3
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	32-39	8	19
β-strand	46-52	7	19
β-strand	56-59	4	19
α-helix	61-63	3
β-strand	67-72	6	18
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-96	9	19
α-helix	100-100B	3
β-strand	102-103	2	19
β-strand	104	1	18
β-strand	107-111	5	19
α-helix	115-116	2
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
β-strand	135-145	11	21
β-strand	146	1	20
β-strand	151-154	4	22
α-helix	155-157	3
β-strand	159	1	22
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-170	2	21
β-strand	176-185	10	21
α-helix	186-188	3
β-strand	195-200	6	22
β-strand	205-210	6	22

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-127	6
β-strand	130-139	10	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-154	2	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-181	9	16
α-helix	183-186	4
β-strand	191-197	7	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP120	G	protein	321	Human immunodeficiency virus 1	P04578 (AlphaFold model)
T-cell surface glycoprotein CD4	C	protein	185	Homo sapiens	P01730 (AlphaFold model)
Antibody 17B, light chain	L	protein	214	Homo sapiens
Antibody 17B, heavy chain	H	protein	229	Homo sapiens

Sequence of entity 1 (G), FASTA

>1RZJ_1 ENVELOPE GLYCOPROTEIN GP120 (chains G)
GARSEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVIT
QACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLN
GSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTGAGHCNISRAKWNNTLKQIASKLRE
QFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGS
DTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPG
GGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (C), FASTA

>1RZJ_2 T-CELL SURFACE GLYCOPROTEIN CD4 (chains C)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASNT

Sequence of entity 3 (L), FASTA

>1RZJ_3 ANTIBODY 17B, LIGHT CHAIN (chains L)
DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 4 (H), FASTA

>1RZJ_4 ANTIBODY 17B, HEAVY CHAIN (chains H)
EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12
IPA	Isopropyl alcohol	C3 H8 O	1

Primary citation

Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120. Huang, C.C., Venturi, M., Majeed, S. et al. Proc Natl Acad Sci U S A (2004) 101:2706-2711. DOI 10.1073/pnas.0308527100 · PubMed

Other PDB entries of the same protein (UniProt P04578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8F3A 1.2 Å, HIV-1 gp41 coiled-coil pocket IQN17
6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
9ARN 1.41 Å, Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal…
1DF4 1.45 Å, Interactions between HIV-1 GP41 core and detergents and their implications for membrane…
6BXP 1.45 Å, Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
7EKB 1.45 Å, Crystal structure of 4E10 modified with pyrene acetamide
5X08 1.49 Å, Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with…
6JQK 1.5 Å, Structure of C34M/N36
5TKK 1.55 Å, Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex…
6PDR 1.55 Å, Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion…

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