6VTT: CAP256-VRC26.25 Fab

Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2. Determined by electron microscopy at 3.7 Å resolution. Released 8 Apr 2020.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 8
Atoms: 16,607
Mol. weight: 284.5 kDa
Ligands: NAG
Released: 8 Apr 2020

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

Secondary structure: helices and β-sheets

6VTT contains 51 α-helices and 170 β-strands across 8 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 A: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	514-521	7
α-helix	522-525	4
β-strand	529	1	53
α-helix	530-541	12
α-helix	570-595	26
β-strand	603	1	1
β-strand	609	1	1
α-helix	619-622	4
β-strand	627	1	53
α-helix	628-635	8
α-helix	639-658	20

Chain B: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-540	11
α-helix	570-594	25
β-strand	603-609	7	31
α-helix	619-622	4
α-helix	628-635	8
α-helix	636-638	3
α-helix	641-657	17

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	514-519	5
β-strand	529	1	54
α-helix	533-542	10
α-helix	570-594	25
β-strand	605-609	5	15
α-helix	610	1
α-helix	619-622	4
β-strand	627	1	54
α-helix	628-632	5
α-helix	640-658	19

Chain E: 10 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	15
β-strand	45-47	3	16
β-strand	53	1	17
β-strand	84-85	2	16
β-strand	89	1	18
β-strand	91-93	3	19
α-helix	100-114	15
β-strand	120-121	2	20
α-helix	123-125	3
β-strand	131-132	2	21
β-strand	154-162	9	21
β-strand	169-177	9	21
α-helix	178-180	3
β-strand	181-185	5	22
β-strand	190-193	4	22
β-strand	201	1	23
β-strand	202-203	2	20
β-strand	215	1	24
β-strand	218	1	17
α-helix	219-220	2
β-strand	223-228	6	16
β-strand	237-239	3	19
β-strand	241	1	18
β-strand	242-245	4	16
β-strand	247	1	17
β-strand	251	1	24
β-strand	259	1	25
β-strand	271-273	3	26
α-helix	283	1
β-strand	284-287	4	26
β-strand	292-297	6	27
β-strand	301-308	8	21
β-strand	316-323	9	21
β-strand	330-331	2	27
β-strand	334	1	28
α-helix	336-339	4
α-helix	341-348	8
β-strand	359-361	3	26
β-strand	376-378	3	29
β-strand	381-384	4	29
β-strand	413	1	28
β-strand	416-417	2	27
β-strand	419-420	2	29
β-strand	423-424	2	30
α-helix	426-428	3
β-strand	433	1	23
β-strand	434-435	2	30
α-helix	436-440	5
β-strand	441	1	21
β-strand	444-449	6	27
β-strand	452	1	25
β-strand	453-456	4	26
β-strand	466-470	5	26
α-helix	477-480	4
β-strand	486-491	6	16
β-strand	494-499	6	15

Chain F: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53	1	3
β-strand	56	1	4
α-helix	75	1
β-strand	76	1	4
β-strand	83-85	3	2
β-strand	92-93	2	5
α-helix	100-115	16
α-helix	120	1
β-strand	121	1	6
β-strand	129	1	7
β-strand	130-133	4	8
β-strand	154-158	5	8
β-strand	160-162	3	9
β-strand	169-171	3	9
β-strand	174-177	4	8
β-strand	181-185	5	7
β-strand	190-193	4	7
β-strand	202-203	2	6
β-strand	215	1	10
β-strand	218	1	3
β-strand	223-228	6	2
β-strand	237-238	2	5
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	10
β-strand	259-260	2	11
β-strand	271-273	3	11
β-strand	283-297	15	11
β-strand	301	1	12
β-strand	304-312	7	8
β-strand	315-320	6	8
β-strand	323	1	12
β-strand	330-334	5	11
α-helix	335-348	14
α-helix	349-352	4
β-strand	358-361	4	13
β-strand	374-378	5	14
β-strand	381-385	5	14
β-strand	413-417	5	11
β-strand	418-420	3	14
β-strand	423-424	2	6
α-helix	426-428	3
β-strand	434-435	2	6
α-helix	436-438	3
β-strand	444-455	12	11
β-strand	465-468	4	13
α-helix	476-478	3
β-strand	487-491	5	2
β-strand	494-499	6	1

Chain G: 8 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	31
β-strand	45-47	3	32
β-strand	53	1	33
β-strand	56	1	34
α-helix	75	1
β-strand	76	1	34
β-strand	91-92	2	35
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	36
β-strand	129	1	37
β-strand	132-133	2	38
β-strand	154-162	9	38
β-strand	168-177	10	38
α-helix	178-180	3
β-strand	181-183	3	37
β-strand	191-193	3	37
β-strand	201-203	3	36
β-strand	215	1	39
β-strand	218	1	33
β-strand	223-227	5	32
β-strand	238-239	2	35
β-strand	245	1	32
β-strand	247	1	33
β-strand	251	1	39
β-strand	259	1	40
α-helix	264-266	3
β-strand	271-273	3	40
β-strand	284-287	4	40
β-strand	292-297	6	41
β-strand	304-308	5	38
β-strand	316-320	5	38
β-strand	330-333	4	41
α-helix	335-353	19
β-strand	359-361	3	42
β-strand	377-378	2	43
β-strand	381-385	5	43
β-strand	394	1	42
β-strand	414-417	4	41
β-strand	418-421	4	43
β-strand	423-424	2	36
α-helix	426-428	3
β-strand	433-435	3	36
α-helix	436-439	4
β-strand	444-449	6	41
β-strand	452-455	4	40
β-strand	466-468	3	42
β-strand	469-470	2	40
β-strand	486-491	6	32
β-strand	494-499	6	31

Chain H: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	44
β-strand	10-12	3	45
β-strand	17-20	4	46
β-strand	21-25	5	44
α-helix	29-31	3
β-strand	34-39	6	47
β-strand	45-51	7	47
β-strand	57-59	3	47
α-helix	61-63	3
β-strand	68-71	4	46
β-strand	77	1	44
β-strand	78-82A	6	46
α-helix	84-86	3
β-strand	89-90	2	48
β-strand	91-94	4	47
β-strand	100-100E	6	38
α-helix	100O-100P	2
β-strand	100Q-100U	5	38
β-strand	102-103	2	47
β-strand	107-108	2	48
β-strand	109-111	3	45

Chain L: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	49
β-strand	5	1	50
β-strand	9	1	51
β-strand	19-24	6	50
β-strand	33-38	6	51
β-strand	45-48	4	51
β-strand	49	1	52
β-strand	53	1	52
β-strand	64-67	4	50
β-strand	70-75	6	50
α-helix	80-82	3
β-strand	85-90	6	51
β-strand	97-98	2	51
β-strand	99	1	49
β-strand	102-103	2	51

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	E, F, G	protein	471	Human immunodeficiency virus 1	A0A0N9FF17
VRC26.25 Heavy Chain	H	protein	257	Homo sapiens
VRC26.25 Light Chain	L	protein	217	Homo sapiens	A2NUT2 (AlphaFold model)
Envelope glycoprotein gp41	A, B, C	protein	154	Human immunodeficiency virus 1

Sequence of entity 1 (E, F, G), FASTA

>6VTT_1 Envelope glycoprotein gp120 (chains E, F, G)
GLWVTVYYGVPVWREAKTTLFCASDAKSYEKEVHNVWATHACVPTDPNPQELVLENVTEN
FNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNATYKGTREEIKNCSF
NATTELRDKKRREYALFYRLDIVPLSGEGNNNSEYRLINCNTSVITQICPKVTFDPIPIH
YCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTDNVKTIIVHLNESVEITCTRPNNMTRKSVRIGPGQTFYALGDIIGDIRQPHCNISEIK
WEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFNET
YSTGSNSTNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGGNN
STKETFRPGGGNMRDNWRSELYKYKVVEVKPLGIAPTECNRTVVQRRRRRR

Sequence of entity 2 (H), FASTA

>6VTT_2 VRC26.25 Heavy Chain (chains H)
QVQLVESGGGVVQPGTSLRLSCAASQFRFDGYGMHWVRQAPGKGLEWVASISHDGIKKYH
AEKVWGRFTISRDNSKNTLYLQMNSLRPEDTALYYCAKDLREDECEEWWSDYYDFGKQLP
CAKSRGGLVGIADNWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPE
PVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD
KRVEPKSCDKGLEVLFQ

Sequence of entity 3 (L), FASTA

>6VTT_3 VRC26.25 Light Chain (chains L)
QSVLTQPPSVSAAPGQKVTISCSGNTSNIGNNFVSWYQQRPGRAPQLLIYETDKRPSGIP
DRFSASKSGTSGTLAITGLQTGDEADYYCATWAASLSSARVFGTGTKVIVLVQPKANPTV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (A, B, C), FASTA

>6VTT_4 Envelope glycoprotein gp41 (chains A, B, C)
AVVGLGAVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLGV
WGFKQLQARVLAIERYLEVQQLLGMWGCSGKLICCTNVPWNSSWSNKTYNEIWDNMTWMQ
WDREIGNYTDTIYKLLEVSQFQQEINEKDNLTLD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	41

Primary citation

Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition. Gorman, J., Chuang, G.Y., Lai, Y.T. et al. Cell Rep (2020) 31:107488-107488. DOI 10.1016/j.celrep.2020.03.052 · PubMed

Other PDB entries of the same protein (UniProt A0A0N9FF17), best resolution first:

6VZI 2.72 Å, Crystal Structure of HIV-1 CAP256 RnS-3mut-2G-SOSIP.664 Prefusion Env Trimer in Complex…
6VRW 3.71 Å, Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
7LY9 3.91 Å, Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.wk34.c80 SOSIP.RnS2…
9BTH 4.2 Å, Rhesus Fab 42056-a.01 in complex with CAP256SU.wk34 RnS SOSIP Env

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