6EDU: B41 SOSIP.664

B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195. Determined by electron microscopy at 4.06 Å resolution. Released 17 Oct 2018.

Method: Electron microscopy
Resolution: 4.06 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 21
Atoms: 26,271
Mol. weight: 601.82 kDa
Ligands: NAG
Released: 17 Oct 2018

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

Secondary structure: helices and β-sheets

6EDU contains 51 α-helices and 274 β-strands across 21 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: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	520-522	3
α-helix	530-543	14
α-helix	566-594	29
β-strand	603	1	1
α-helix	619-624	6
α-helix	628-634	7
α-helix	636-651	16

Chains B and C: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	520-522	3
α-helix	530-543	14
α-helix	566-594	29
β-strand	603-605	3	2
α-helix	619-624	6
α-helix	628-634	7
α-helix	636-651	16

Chain D: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-46	2	4
β-strand	53	1	5
α-helix	69-73	5
β-strand	83-85	3	4
β-strand	91-92	2	6
α-helix	101-112	12
β-strand	120-124	5	7
β-strand	127	1	8
β-strand	195	1	8
β-strand	198-202	5	7
β-strand	218	1	5
β-strand	223-227	5	4
β-strand	238-239	2	6
β-strand	243-245	3	4
β-strand	247	1	5
β-strand	256	1	9
β-strand	260-261	2	9
β-strand	271-272	2	9
β-strand	284-297	14	9
β-strand	328-333	6	9
α-helix	338-351	14
β-strand	357-359	3	10
α-helix	369-372	4
β-strand	373-378	6	9
β-strand	381-386	6	9
β-strand	415-420	6	9
β-strand	423-425	3	7
α-helix	426	1
β-strand	432-434	3	7
β-strand	444-454	11	9
β-strand	465-467	3	10
β-strand	470	1	9
α-helix	477-480	4
β-strand	487-491	5	4
β-strand	494-499	6	1

Chain E: 6 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	3
β-strand	45-46	2	11
β-strand	53	1	12
α-helix	69-73	5
β-strand	83-85	3	11
β-strand	91-92	2	13
α-helix	101-112	12
β-strand	120-124	5	14
β-strand	127	1	15
β-strand	158-160	3	16
β-strand	171-172	2	16
β-strand	195	1	15
β-strand	198-202	5	14
β-strand	218	1	12
β-strand	223-227	5	11
β-strand	238-239	2	13
β-strand	243-245	3	11
β-strand	247	1	12
β-strand	256	1	17
β-strand	260-261	2	17
β-strand	271-272	2	17
β-strand	284-297	14	17
β-strand	328-333	6	17
α-helix	338-351	14
β-strand	357-359	3	18
α-helix	369-372	4
β-strand	373-378	6	17
β-strand	381-386	6	17
β-strand	415-420	6	17
β-strand	423-425	3	14
α-helix	426	1
β-strand	432-434	3	14
β-strand	444-454	11	17
β-strand	465-467	3	18
β-strand	470	1	17
α-helix	477-480	4
β-strand	487-491	5	11
β-strand	494-499	6	3

Chain F: 6 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-46	2	19
β-strand	53	1	20
α-helix	69-73	5
β-strand	83-85	3	19
β-strand	91-92	2	21
α-helix	101-112	12
β-strand	120-124	5	22
β-strand	127	1	23
β-strand	159	1	24
β-strand	172	1	24
β-strand	195	1	23
β-strand	198-202	5	22
β-strand	218	1	20
β-strand	223-227	5	19
β-strand	238-239	2	21
β-strand	243-245	3	19
β-strand	247	1	20
β-strand	256	1	25
β-strand	260-261	2	25
β-strand	271-272	2	25
β-strand	284-297	14	25
β-strand	328-333	6	25
α-helix	338-351	14
β-strand	357-359	3	26
α-helix	369-372	4
β-strand	373-378	6	25
β-strand	381-386	6	25
β-strand	415-420	6	25
β-strand	423-425	3	22
α-helix	426	1
β-strand	432-434	3	22
β-strand	444-454	11	25
β-strand	465-467	3	26
β-strand	470	1	25
α-helix	477-480	4
β-strand	487-491	5	19
β-strand	494-499	6	2

Chains G, H and I: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	27
β-strand	12-17	6	28
β-strand	27-29	3	29
β-strand	35	1	29
β-strand	55-56	2	28
α-helix	60-62	3
β-strand	66-71	6	28
α-helix	76-78	3
β-strand	81-82	2	27
β-strand	83-85	3	29
β-strand	93-96	4	27

Chains J, L and N: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	36
β-strand	10-12	3	37
β-strand	17-25	9	36
β-strand	34-39	6	37
β-strand	45-49	5	37
β-strand	51	1	38
β-strand	58	1	38
β-strand	68-73	6	36
β-strand	78-84	7	36
β-strand	92-98	7	37
β-strand	114-115	2	37
β-strand	119-123	5	37

Chains K, M and O: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	39
β-strand	10-13	4	40
β-strand	19-24	6	39
β-strand	36-40	5	40
α-helix	45-46	2
β-strand	47-50	4	40
β-strand	51	1	41
β-strand	55	1	41
α-helix	61-63	3
β-strand	64-69	6	39
β-strand	72-77	6	39
β-strand	87-93	7	40
β-strand	101-103	3	40
β-strand	108-111	4	40

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	A, B, C	protein	153	Human immunodeficiency virus 1	B3UEZ6
Envelope glycoprotein gp160	D, E, F	protein	516	Human immunodeficiency virus 1	B3UES2
T-cell surface glycoprotein CD4	G, H, I	protein	185	Homo sapiens	P01730 (AlphaFold model)
21c Fab VH domain	J, L, N	protein	231	Homo sapiens
21c Fab VL domain	K, M, O	protein	217	Homo sapiens
8ANC195 G52K5 Fab VH domain	P, R, T	protein	244	Homo sapiens
8ANC195 G52K5 Fab VL domain	Q, S, U	protein	215	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>6EDU_1 Envelope glycoprotein gp160 (chains A, B, C)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 2 (D, E, F), FASTA

>6EDU_2 Envelope glycoprotein gp160 (chains D, E, F)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV

Sequence of entity 3 (G, H, I), FASTA

>6EDU_3 T-cell surface glycoprotein CD4 (chains G, H, I)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASNT

Sequence of entity 4 (J, L, N), FASTA

>6EDU_4 21c Fab VH domain (chains J, L, N)
QVQVVQSGAEVRKPGASVKVSCKVSGFTLTGLSIHWVRQAPGKGLEWMGGFGPEENEIIY
AQKFQGRVSMTEDTSTNTAYMELSSLRSEDTAVYYCATGGNYYNLWTGYYPLAYWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT

Sequence of entity 5 (K, M, O), FASTA

>6EDU_5 21c Fab VL domain (chains K, M, O)
QSVLTQPPSVSAAPGQKVTISCSGSSSNIGKNYVSWYQQLPGAAPKLLIFDDTQRPSGIP
DRFSGSKSGTSATLAITGLQTGDEADYYCGTWDSSLSTGQLFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTMAHAECS

Sequence of entity 6 (P, R, T), FASTA

>6EDU_6 8ANC195 G52K5 Fab VH domain (chains P, R, T)
QIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSAS
HHFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDKWSGLHHDGVMAFS
SWGQGTLISVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHH
HHHH

Sequence of entity 7 (Q, S, U), FASTA

>6EDU_7 8ANC195 G52K5 Fab VL domain (chains Q, S, U)
DIQMTQSPSTLSASIGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVP
SRFSGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27

Primary citation

Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion. Wang, H., Barnes, C.O., Yang, Z. et al. Cell Host Microbe (2018) 24:579-592.e4. DOI 10.1016/j.chom.2018.09.003 · PubMed

Other PDB entries of the same protein (UniProt B3UEZ6), best resolution first:

6MUF 2.91 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human…
6MUG 2.95 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6OKP 3.28 Å, B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody…
6OPN 3.5 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35
6OPO 3.5 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
5VN8 3.6 Å, Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain…
6X5B 3.6 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule…
5VN3 3.7 Å, Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen…
6OPP 3.7 Å, Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
6OPQ 3.8 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG
6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
6X5C 4.04 Å, Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52

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