6MFT: Glycosylated 426c HIV-1 gp120 core G459C

Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01 A60C heavy chain. Determined by X-ray diffraction at 2.31 Å resolution. Released 14 Nov 2018.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Homo sapiens
Chains: 6
Atoms: 12,470
Mol. weight: 180.02 kDa
Ligands: NAG, CIT
Released: 14 Nov 2018

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

Secondary structure: helices and β-sheets

6MFT contains 36 α-helices and 147 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 A: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	17-25	9	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-51	7	14
β-strand	57-59	3	14
β-strand	67-72	6	13
β-strand	77-82A	7	13
α-helix	84-86	3
β-strand	88-95	8	14
β-strand	100D-103	4	14
β-strand	107-111	5	14
β-strand	117	1	15
α-helix	118-119	2
β-strand	120-124	5	16
β-strand	135-145	11	16
β-strand	146	1	15
β-strand	151	1	17
β-strand	154	1	17
α-helix	155-157	3
β-strand	163-165	3	16
α-helix	166-168	3
β-strand	169-170	2	16
β-strand	176-185	10	16
β-strand	195-200	6	17
β-strand	205-210	6	17

Chain B: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	34-38	5	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	19
β-strand	97-98	2	19
β-strand	102-108	5	19
β-strand	113	1	20
β-strand	116-120	5	21
α-helix	124-127	4
β-strand	132-141	10	21
β-strand	142	1	20
β-strand	146-152	7	22
β-strand	155-156	2	22
β-strand	161-165	5	21
α-helix	167-169	3
β-strand	175-183	9	21
α-helix	185-188	4
β-strand	193-200	8	22
β-strand	207-212	6	22

Chain C: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	30
α-helix	65-73	9
β-strand	75-76	2	30
α-helix	77-78	2
β-strand	84-86	3	31
β-strand	91-94	4	32
α-helix	99-115	17
β-strand	120-123	4	33
β-strand	199-202	4	33
α-helix	212-214	3
β-strand	215	1	34
β-strand	216-218	3	30
β-strand	223-228	6	31
β-strand	236-239	4	32
β-strand	242-245	4	31
β-strand	247	1	30
β-strand	251	1	34
β-strand	259-261	3	35
β-strand	271-273	3	35
β-strand	284-298	15	35
β-strand	328-329	2	36
β-strand	330-334	5	35
α-helix	335-352	18
β-strand	358-360	3	35
α-helix	368-371	4
β-strand	373-377	5	36
β-strand	380-384	5	36
β-strand	413-415	3	35
β-strand	418-421	4	36
β-strand	423-425	3	33
β-strand	432-434	3	33
α-helix	436-439	4
β-strand	443-456	14	35
β-strand	466-470	5	35
α-helix	475-483	9
β-strand	486-490	5	31

Chain G: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	23
α-helix	65-73	9
β-strand	75-76	2	23
β-strand	84-85	2	24
β-strand	89	1	25
β-strand	91-94	4	26
α-helix	99-115	17
β-strand	120-123	4	27
β-strand	199-202	4	27
β-strand	215	1	28
β-strand	216-218	3	23
β-strand	223-228	6	24
β-strand	236-239	4	26
β-strand	241	1	25
β-strand	242-245	4	24
β-strand	247	1	23
β-strand	251	1	28
β-strand	256	1	29
β-strand	259-261	3	29
α-helix	264-266	3
β-strand	271-273	3	29
β-strand	284-298	15	29
β-strand	328-333	6	29
α-helix	335-350	16
β-strand	357-360	4	29
α-helix	368-371	4
β-strand	373-377	5	29
β-strand	380-384	5	29
β-strand	414-421	8	29
β-strand	423-425	3	27
β-strand	432-434	3	27
α-helix	436-439	4
β-strand	443-456	14	29
β-strand	465-470	6	29
α-helix	476-483	8
β-strand	486-490	5	24

Chain H: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	100D-103	4	2
β-strand	107-111	5	2
β-strand	117	1	3
β-strand	120	1	4
β-strand	123-124	2	5
β-strand	135-145	11	5
β-strand	146	1	3
β-strand	151-154	4	6
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	194-195	2	7
β-strand	196-200	5	6
β-strand	205-207	3	6
β-strand	210-211	2	7

Chain L: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	34-38	5	9
β-strand	45-49	5	9
β-strand	53-54	2	9
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-90	6	9
β-strand	97-98	2	9
β-strand	102-108	5	9
β-strand	113	1	10
β-strand	116-120	5	11
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	11
β-strand	142	1	10
β-strand	147-152	6	12
β-strand	155-156	2	12
β-strand	161-165	5	11
α-helix	166-169	4
β-strand	175-184	10	11
α-helix	185-190	6
β-strand	193-199	7	12
β-strand	207	1	12
β-strand	210-212	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy Chain glVRC01	A, H	protein	233	Homo sapiens
Light chain glVRC01	B, L	protein	210	Homo sapiens
Gp120	C, G	protein	347	Homo sapiens	M4Q8P8

Sequence of entity 1 (A, H), FASTA

>6MFT_1 Heavy Chain glVRC01 (chains A, H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY
CQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKNSDYNWDFQHWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 2 (B, L), FASTA

>6MFT_2 Light chain glVRC01 (chains B, L)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQYEFFGQGTKLEIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, G), FASTA

>6MFT_3 Gp120 (chains C, G)
VWKEAKTTLFCASDAKAYEKECHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQ
MQEDVISIWDQCLKPCVKLTNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGK
GPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLSDNAKIIIVQLNKSVEIVC
TRPNNGGSGSGGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITT
HSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKAIYAPPIKGNITCKS
DITGLLLLRDGCNTTNNTEIFRPGGGDMRDNWRSELYKYKVVEIKPL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13
CIT	Citric acid	C6 H8 O7	1

Water and common crystallization additives (PEG, EDO) are not listed.

Primary citation

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. Borst, A.J., Weidle, C.E., Gray, M.D. et al. Elife (2018) 7. DOI 10.7554/eLife.37688 · PubMed

Other PDB entries of the same protein (UniProt M4Q8P8), best resolution first:

5FA2 2.0 Å, Crystal structure of 426c.TM4deltaV1-3 p120
6P8M 3.59 Å, Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex with 426c HIV-1 gp120…
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

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