9BTH: Rhesus Fab 42056-a.01

Rhesus Fab 42056-a.01 in complex with CAP256SU.wk34 RnS SOSIP Env. Determined by electron microscopy at 4.2 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Macaca mulatta, Human immunodeficiency virus 1
Chains: 8
Atoms: 16,629
Mol. weight: 285.2 kDa
Ligands: NAG
Released: 11 Jun 2025

Explore 9BTH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BTH contains 63 α-helices and 157 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 B: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	517-523	7
α-helix	530-536	7
α-helix	537-540	4
α-helix	570-596	27
β-strand	603-609	7	33
α-helix	612-614	3
α-helix	619-622	4
α-helix	628-635	8
α-helix	639-661	23

Chain C: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	516-519	4
α-helix	521-523	3
β-strand	529	1	20
α-helix	530-533	4
α-helix	538-540	3
α-helix	571-595	25
β-strand	603-609	7	6
α-helix	619-622	4
β-strand	627	1	20
α-helix	628-635	8
α-helix	639-661	23

Chain D: 13 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	21
β-strand	45-47	3	22
β-strand	53-55	3	23
β-strand	67	1	24
β-strand	75	1	23
β-strand	84	1	22
β-strand	91-92	2	25
α-helix	101-106	6
α-helix	109-116	8
α-helix	120	1
β-strand	121	1	26
α-helix	123-125	3
β-strand	129-130	2	27
β-strand	154-162	9	27
β-strand	169-177	9	27
β-strand	181-183	3	27
β-strand	190-193	4	27
α-helix	194-196	3
β-strand	202-203	2	26
β-strand	209	1	24
β-strand	216-218	3	23
β-strand	221	1	28
β-strand	223	1	28
β-strand	224-228	5	22
β-strand	238-239	2	25
β-strand	242-245	4	22
β-strand	247	1	23
β-strand	256	1	29
β-strand	259	1	30
α-helix	263-266	4
β-strand	271-273	3	31
α-helix	283	1
β-strand	284-287	4	31
β-strand	292-298	7	32
β-strand	304-308	5	27
β-strand	316-320	5	27
α-helix	328-329	2
β-strand	330-333	4	32
α-helix	335-353	19
β-strand	359-361	3	31
β-strand	374-377	4	29
β-strand	382-385	4	29
β-strand	414-415	2	32
β-strand	418-420	3	29
β-strand	423-424	2	26
α-helix	426-428	3
β-strand	434-435	2	26
α-helix	437-439	3
β-strand	443-449	7	32
β-strand	452	1	30
β-strand	453-456	4	31
β-strand	466-470	5	31
α-helix	475-479	5
α-helix	480-483	4
β-strand	486-491	6	22
β-strand	494-499	6	21

Chain E: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	519-523	5
α-helix	533-539	7
α-helix	570-595	26
β-strand	603-609	7	21
α-helix	619-622	4
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-662	24

Chain F: 12 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	33
β-strand	45-47	3	34
β-strand	53	1	35
β-strand	56	1	36
β-strand	67	1	37
β-strand	76	1	36
β-strand	84	1	34
β-strand	92-94	3	38
α-helix	100-115	16
α-helix	120	1
β-strand	121	1	39
α-helix	123-125	3
β-strand	129-133	5	40
β-strand	154-162	9	40
β-strand	169-177	9	40
α-helix	178-180	3
β-strand	181-183	3	40
β-strand	190-193	4	40
β-strand	201-203	3	39
α-helix	204-205	2
β-strand	209	1	37
β-strand	215	1	41
β-strand	218	1	35
α-helix	219-220	2
β-strand	223-228	6	34
β-strand	236-238	3	38
β-strand	242-245	4	34
β-strand	247	1	35
β-strand	251	1	41
β-strand	256	1	42
β-strand	259-261	3	43
α-helix	263-266	4
β-strand	271-273	3	43
β-strand	283-297	15	43
β-strand	298	1	44
β-strand	302-307	6	40
β-strand	317-322	7	40
β-strand	330-333	4	43
α-helix	335-348	14
α-helix	350-352	3
β-strand	359-361	3	43
β-strand	374-378	5	42
β-strand	381-385	5	42
β-strand	414-417	4	43
β-strand	418-419	2	42
β-strand	423-424	2	39
β-strand	433-435	3	39
α-helix	437-439	3
β-strand	443	1	44
β-strand	446-456	11	43
β-strand	466-470	5	43
α-helix	476-482	7
α-helix	483-485	3
β-strand	488-491	4	34
β-strand	496-499	4	33

Chain G: 10 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	6
β-strand	45-47	3	7
β-strand	53-56	4	8
β-strand	75-76	2	8
β-strand	91-94	4	9
α-helix	95-97	3
α-helix	99-106	8
α-helix	109-116	8
β-strand	121	1	10
α-helix	123-125	3
β-strand	129	1	11
β-strand	130-132	3	12
β-strand	154-159	6	12
β-strand	162	1	13
β-strand	169	1	13
β-strand	172-177	6	12
β-strand	181-182	2	14
β-strand	191	1	11
β-strand	192-193	2	14
α-helix	194-197	4
β-strand	200-203	4	10
β-strand	215	1	15
β-strand	216-218	3	8
α-helix	219-220	2
β-strand	221	1	7
β-strand	223-228	6	7
β-strand	236-239	4	9
β-strand	242-245	4	7
β-strand	247	1	8
β-strand	251	1	15
β-strand	259-261	3	16
α-helix	263-266	4
β-strand	272-274	3	16
β-strand	283	1	17
β-strand	284-298	15	16
β-strand	301-308	8	18
β-strand	316-323	9	18
β-strand	330-334	5	16
α-helix	335-350	16
β-strand	359-361	3	17
β-strand	376	1	19
β-strand	383-385	3	19
β-strand	408-415	3	16
β-strand	418-420	3	19
β-strand	423-424	2	10
β-strand	432-435	4	10
α-helix	436-439	4
β-strand	443-452	10	16
β-strand	454-456	3	17
β-strand	466-470	5	17
α-helix	476-480	5
β-strand	488-491	4	7
β-strand	495-499	5	6

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	8	3
β-strand	45-51	7	3
β-strand	58-59	2	3
α-helix	61-66	6
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-100A	14	3
β-strand	100F-103	11	3
β-strand	107-109	3	3
β-strand	110-111	2	2

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	10-11	2	5
β-strand	19-24	6	4
β-strand	33-38	6	5
α-helix	43-44	2
β-strand	45-49	5	5
β-strand	53-54	2	5
β-strand	62-66	5	4
β-strand	70-75	6	4
α-helix	80-82	3
β-strand	84-90	7	5
α-helix	96	1
β-strand	97-98	2	5
β-strand	103-104	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy	H	protein	244	Macaca mulatta
Light	L	protein	220	Macaca mulatta
Envelope glycoprotein gp120	D, F, G	protein	471	Human immunodeficiency virus 1	A0A0N9FF17
Envelope glycoprotein gp41	B, C, E	protein	154	Human immunodeficiency virus 1	A0A6M2Z8U6

Sequence of entity 1 (H), FASTA

>9BTH_1 Heavy (chains H)
QVQLQESGPGMVKPSETLTLTCAVFGGRVTSGDSFWTWIRQSPTKGLEWLAGISGDADNP
TYNPSLKSRLTISKDPSKNQVSLKVTSVTATDTAVYYCAREKQYYFDDYYSVESGRVGMD
SWGQGVAVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ

Sequence of entity 2 (L), FASTA

>9BTH_2 Light (chains L)
DIVMTQTPISLPVSLGESATISCRSSRSLVDRQDGKTYLEWYFQKPGQSPQLLIYEVANR
ASGVPDRFRGSGSDTDFTLKISRVEADDVAIYYCMQSLDPPHTFGQGTKVEIRRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D, F, G), FASTA

>9BTH_3 Envelope glycoprotein gp120 (chains D, F, G)
GLWVTVYYGVPVWREAKTTLFCASDAKSYEKEVHNVWATHACVPTDPNPQELVLENVTEN
FNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNATYKGTREEIKNCSF
NATTELRDKKRREYALFYRLDIVPLSGEGNNNSEYRLINCNTSVITQICPKVTFDPIPIH
YCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTDNVKTIIVHLNESVEITCTRPNNMTRKSVRIGPGQTFYALGDIIGDIRQPHCNISEIK
WEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFNET
YSTGSNSTNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGGNN
STKETFRPGGGNMRDNWRSELYKYKVVEVKPLGIAPTECNRTVVQRRRRRR

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

>9BTH_4 Envelope glycoprotein gp41 (chains B, C, E)
AVVGLGAVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLGV
WGFKQLQARVLAIERYLEVQQLLGMWGCSGKLICCTNVPWNSSWSNKTYNEIWDNMTWMQ
WDREIGNYTDTIYKLLEVSQFQQEINEKDNLTLD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	56

Primary citation

Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies. Roark, R.S., Habib, R., Gorman, J. et al. J Exp Med (2025) 222. DOI 10.1084/jem.20250638 · 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…
6VTT 3.7 Å, Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80…
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…

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