6VZI: Envelope glycoprotein gp41

Crystal Structure of HIV-1 CAP256 RnS-3mut-2G-SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom. Determined by X-ray diffraction at 2.72 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 2.72 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 9,915
Mol. weight: 154.45 kDa
Ligands: NAG
Released: 15 Apr 2020

Explore 6VZI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VZI contains 33 α-helices and 119 β-strands across 6 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 B: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	523-525	3
α-helix	530-534	5
α-helix	572-594	23
β-strand	603-609	7	1
α-helix	628-634	7
α-helix	639-660	22

Chain D: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	2
β-strand	20-25	6	2
β-strand	27	1	2
β-strand	34-40	7	3
β-strand	46-51	6	3
β-strand	57-59	3	3
β-strand	67-72D	10	2
β-strand	74-82	9	2
β-strand	88-94	7	3
β-strand	102-103	2	3
β-strand	104	1	2
β-strand	107-108	2	3

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	4
β-strand	5-6	2	5
β-strand	9	1	6
β-strand	18-21	4	7
β-strand	23-24	2	5
β-strand	32	1	8
β-strand	35-38	4	6
β-strand	45-49	5	6
β-strand	53-54	2	6
α-helix	55	1
β-strand	62-66	5	7
β-strand	71-76	6	7
α-helix	80-82	3
β-strand	85-88	4	6
β-strand	91	1	8
β-strand	99	1	4
β-strand	102-103	2	6

Chain G: 14 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45	1	9
β-strand	53-56	4	10
β-strand	67	1	11
β-strand	75-76	2	10
α-helix	77-78	2
β-strand	83-85	3	12
β-strand	90-94	5	13
α-helix	95-97	3
α-helix	99-115	17
β-strand	121	1	14
α-helix	123-125	3
β-strand	129-133	5	15
β-strand	154-162	9	15
β-strand	169-177	9	15
α-helix	178-180	3
β-strand	181-183	3	15
β-strand	190-193	4	15
α-helix	194-196	3
β-strand	200-203	4	14
β-strand	209	1	11
β-strand	215	1	16
β-strand	216-218	3	10
α-helix	219-220	2
β-strand	223-227	5	12
β-strand	236-240	5	13
β-strand	243-245	3	12
β-strand	247	1	10
α-helix	248-250	3
β-strand	251	1	16
β-strand	260-261	2	15
β-strand	272-273	2	17
α-helix	283	1
β-strand	284	1	18
β-strand	285-286	2	17
β-strand	287-312	24	15
β-strand	315-322	9	15
β-strand	330-334	5	15
α-helix	335-352	18
β-strand	359	1	19
α-helix	369-372	4
β-strand	374-379	6	20
β-strand	381-385	5	20
β-strand	413-417	5	15
β-strand	418-421	4	20
β-strand	423-424	2	14
α-helix	426-428	3
β-strand	432-435	4	14
α-helix	437-440	4
β-strand	441-451	11	15
β-strand	454-456	3	18
β-strand	467	1	19
β-strand	468-470	3	18
α-helix	476-483	8
β-strand	486-490	5	12
β-strand	491	1	9
β-strand	494-499	6	1

Chain H: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	21
β-strand	6-7	2	22
β-strand	11-12	2	23
β-strand	18-23	6	22
β-strand	25	1	21
α-helix	29-31	3
β-strand	33-39	7	24
β-strand	45-51	7	24
β-strand	57-59	3	24
α-helix	64-66	3
β-strand	67-68	2	22
β-strand	71-72	2	22
α-helix	73-75	3
β-strand	77-82	6	22
α-helix	84-86	3
β-strand	89-100A	13	24
β-strand	100J-101	10	24
β-strand	105-106	2	24
β-strand	108-109	2	23
α-helix	113-114	2
β-strand	115	1	25
β-strand	119-122	4	26
β-strand	133-143	11	26
β-strand	144	1	25
β-strand	149-152	4	27
α-helix	153-155	3
β-strand	157	1	27
β-strand	161-168	8	26
β-strand	174-183	10	26
β-strand	192-197	6	27
β-strand	205-209	5	27

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	28
β-strand	18-22	5	29
β-strand	32-38	7	28
β-strand	45-48	4	28
β-strand	62-63	2	29
β-strand	67C	1	30
β-strand	69	1	30
β-strand	72-76	5	29
α-helix	80-82	3
β-strand	85-91	7	28
β-strand	97	1	24
β-strand	102-107	6	28
α-helix	109-111	3
β-strand	112	1	31
β-strand	117-119	3	32
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	32
β-strand	141	1	31
β-strand	145-146	2	33
β-strand	149-151	3	33
β-strand	154-156	3	33
β-strand	160-162	3	32
α-helix	163-165	3
β-strand	166-167	2	32
β-strand	173-181	9	32
α-helix	183-187	5
β-strand	192-198	7	33
β-strand	201-207	7	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp41	B	protein	154	Human immunodeficiency virus 1	W6ICH7
35O22 scFv heavy chain	D	protein	134	Homo sapiens
35O22 scFv light chain	E	protein	114	Homo sapiens
Envelope glycoprotein gp160	G	protein	471	Human immunodeficiency virus 1	A0A0N9FF17
3H109L Fab heavy chain	H	protein	244	Homo sapiens
3H109L Fab light chain	L	protein	217	Homo sapiens

Sequence of entity 1 (B), FASTA

>6VZI_1 Envelope glycoprotein gp41 (chains B)
AVVGLGAVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLGV
WGFKQLQARVLAIERYLEVQQLLGMWGCSGKLICCTNVPWNSSWSNKTYNEIWDNMTWMQ
WDREIGNYTDTIYKLLEVSQFQQEINEKDLLALD

Sequence of entity 2 (D), FASTA

>6VZI_2 35O22 scFv heavy chain (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVNMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSAST

Sequence of entity 3 (E), FASTA

>6VZI_3 35O22 scFv light chain (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQS

Sequence of entity 4 (G), FASTA

>6VZI_4 Envelope glycoprotein gp160 (chains G)
GLWVTVYYGVPVWREAKTTLFCASDAKSYEKEVHNVWATHACVPTDPNPQELVLENVTEN
FNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNATYKGTREEIKNCSF
NATTELRDKKRREYALFYRLDIVPLSGEGNNNSEYRLINCNTSVITQICPKVTFDPIPIH
YCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTDNVKTIIVHLNESVEITCTRPNNMTRKSVRIGPGQTFYALGDIIGDIRQPHCNISEIK
WEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFNET
YSTGSNSTNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGGNN
STKETFRPGGGNMRDNWRSELYKYKVVEVKPLGIAPTECRRRVVQRRRRRR

Sequence of entity 5 (H), FASTA

>6VZI_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ

Sequence of entity 6 (L), FASTA

>6VZI_6 3H109L Fab light chain (chains L)
SVTSYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERF
SGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPMQWKMHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Development of a 3Mut-Apex-Stabilized Envelope Trimer That Expands HIV-1 Neutralization Breadth When Used To Boost Fusion Peptide-Directed Vaccine-Elicited Responses. Chuang, G.Y., Lai, Y.T., Boyington, J.C. et al. J Virol (2020) 94. DOI 10.1128/JVI.00074-20 · PubMed

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