6MET: Coreceptor recognition by HIV-1 envelope spike

Structural basis of coreceptor recognition by HIV-1 envelope spike. Determined by electron microscopy at 4.5 Å resolution. Released 12 Dec 2018.

Method: Electron microscopy
Resolution: 4.5 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 8,911
Mol. weight: 134.83 kDa
Ligands: A2G, NAG
Released: 12 Dec 2018

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

Secondary structure: helices and β-sheets

6MET contains 33 α-helices and 79 β-strands across 3 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, 38 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	13
β-strand	12-13	2	14
β-strand	27-30	4	15
β-strand	35-38	4	15
β-strand	39-40	2	16
β-strand	43-44	2	16
β-strand	45	1	12
β-strand	55-56	2	14
α-helix	59-63	5
β-strand	70-71	2	14
β-strand	82-84	3	15
β-strand	92	1	15
β-strand	96-97	2	13
β-strand	99-101	3	17
β-strand	108-109	2	18
α-helix	112-113	2
β-strand	114-115	2	19
β-strand	117-119	3	17
α-helix	120-121	2
β-strand	128-131	4	20
β-strand	139	1	20
β-strand	145-146	2	19
α-helix	151-153	3
β-strand	158-161	4	20
β-strand	163	1	21
β-strand	166	1	21
β-strand	176-177	2	18
β-strand	183-189	7	22
α-helix	192-193	2
β-strand	194-198	5	23
β-strand	209-217	9	22
β-strand	228-231	4	22
β-strand	237-238	2	22
β-strand	248-249	2	23
β-strand	255-259	5	23
α-helix	264-266	3
β-strand	268-276	9	22
β-strand	281-294	14	22
β-strand	301-306	6	22
β-strand	314-318	5	24
β-strand	324-328	5	24
β-strand	332-335	4	22
β-strand	341-348	8	24
β-strand	353-361	9	24

Chain B: 17 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	33-54	22
α-helix	55-59	5
α-helix	64-80	17
α-helix	83-90	8
α-helix	101-130	30
α-helix	133-139	7
α-helix	142-158	17
α-helix	161-164	4
β-strand	170	1	25
β-strand	177	1	25
β-strand	180	1	10
α-helix	187-199	13
α-helix	200-204	5
α-helix	205-223	19
α-helix	228-259	32
α-helix	271-287	17
α-helix	288-291	4
α-helix	292-299	8
α-helix	306-312	7

Chain G: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	45-46	2	1
α-helix	49-51	3
β-strand	52-55	4	2
α-helix	64-71	8
β-strand	74	1	2
α-helix	75-77	3
β-strand	83-84	2	1
α-helix	85	1
β-strand	88	1	3
β-strand	90	1	4
α-helix	100-114	15
β-strand	119-125	7	5
β-strand	196-202	7	5
β-strand	215-218	4	2
β-strand	223-228	6	1
β-strand	239	1	4
β-strand	241	1	3
β-strand	242-245	4	1
β-strand	247	1	2
β-strand	251	1	2
β-strand	257	1	6
α-helix	264-266	3
β-strand	271-273	3	7
β-strand	284-287	4	7
β-strand	294-297	4	8
β-strand	303	1	9
β-strand	307	1	10
β-strand	321	1	9
β-strand	327-333	7	8
α-helix	334-352	19
β-strand	357-359	3	11
β-strand	365	1	12
α-helix	367-370	4
β-strand	372-376	5	6
β-strand	379-383	5	6
α-helix	386-388	3
β-strand	392	1	11
β-strand	408-414	7	8
β-strand	415	1	6
β-strand	419-420	2	5
β-strand	427-429	3	5
β-strand	439-442	4	8
β-strand	446-449	4	7
β-strand	452	1	11
β-strand	462-464	3	11
β-strand	466	1	7
α-helix	471-476	6
β-strand	482-486	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	G	protein	461	Human immunodeficiency virus 1	Q70145
T-cell surface glycoprotein CD4	A	protein	363	Homo sapiens	P01730 (AlphaFold model)
C-C chemokine receptor type 5	B	protein	313	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>6MET_1 Envelope glycoprotein gp160 (chains G)
DNLWVTVYYGVPVWKEATTTLFCASDAKAYKAEVHNVWATHACVPTDPNPQEIVLENVTE
NFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCIDLNNSTNNNNSSGVKTGID
KGEIKNCSFNTTTSVKDKEKKEYALFYNLDVVQIGNDNTSYRLTSCNTSVITQACPKVTF
EPIPIHYCTPAGYAILKCNGKKFNGTGPCTNVSTVQCTHGIKPVVSTQLLLNGSLAEEDI
VIRSENLTNNAKTIIVQLKDPVDINCTRPNNNTRKSIHIGPGRAFYATGDIIGDIRQAHC
NLSRAQWNDTLSKIVTKLREQFENKTIKFQPPSGGDPEIVFHSFNCGGEFFYCNTTQLFN
STWTNNTEGTSNTTGNDTITLPCRIKQIVNMWQEVGKAMYAPPIKGKIKCSSNITGLLLT
RDGGNNEMNTTEIFRPGGGDMRDNWRSELYKYKVVRIEPLG

Sequence of entity 2 (A), FASTA

>6MET_2 T-cell surface glycoprotein CD4 (chains A)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKR
VTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKN
LTCEVWGPTSPKLMLSLKLENKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIK
VLP

Sequence of entity 3 (B), FASTA

>6MET_3 C-C chemokine receptor type 5 (chains B)
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSS
HFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTI
MIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFV
GEKFRNYLLVFFQ

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Structural basis of coreceptor recognition by HIV-1 envelope spike. Shaik, M.M., Peng, H., Lu, J. et al. Nature (2018) 565:318-323. DOI 10.1038/s41586-018-0804-9 · PubMed

Other PDB entries of the same protein (UniProt Q70145), best resolution first:

6MEO 3.9 Å, Structural basis of coreceptor recognition by HIV-1 envelope spike

Browse structure collections

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