5W1M: MACV GP1 CR1-07 Fab complex

MACV GP1 CR1-07 Fab complex. Determined by X-ray diffraction at 3.91 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 3.91 Å
Organisms: Homo sapiens, Machupo virus
Chains: 12
Atoms: 18,425
Mol. weight: 265.98 kDa
Ligands: NAG, BMA
Released: 30 May 2018

Explore 5W1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W1M contains 93 α-helices and 226 β-strands across 12 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.

Chains A and E: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30-31	2	3
β-strand	38-39	2	3
β-strand	41-46	6	2
α-helix	51-52	2
β-strand	53-57	5	2
β-strand	61-62	2	2
α-helix	63	1
β-strand	70-75	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
α-helix	104	1
β-strand	105-106	2	2
β-strand	110-114	5	2
β-strand	119	1	4
α-helix	120-121	2
β-strand	122-126	5	5
α-helix	127-129	3
α-helix	130-134	5
β-strand	137-147	11	5
β-strand	148	1	4
β-strand	153-158	6	6
β-strand	161-163	3	6
β-strand	167-171	5	5
α-helix	172-175	4
β-strand	181-190	10	5
α-helix	191-195	5
β-strand	199-205	7	6
β-strand	213-218	6	6

Chain B: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	58-60	3	9
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	9
α-helix	105-107	3
β-strand	111-114	4	9
β-strand	118-120	3	9
β-strand	121-122	2	8
α-helix	125-127	3
β-strand	128	1	10
β-strand	131-135	5	11
β-strand	146-156	11	11
β-strand	157	1	10
β-strand	162-165	4	12
α-helix	166-168	3
β-strand	170	1	12
β-strand	174-176	3	11
α-helix	177-179	3
β-strand	180-181	2	11
β-strand	187-196	10	11
α-helix	197-201	5
β-strand	205-211	7	12
β-strand	216-217	2	12
β-strand	220-222	3	12

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-12	3	14
β-strand	19-25	7	13
β-strand	30-31	2	15
α-helix	36-37	2
β-strand	38-39	2	15
β-strand	41-46	6	14
α-helix	51-52	2
β-strand	53-57	5	14
β-strand	61-62	2	14
α-helix	63	1
β-strand	70-75	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-98	7	14
α-helix	104	1
β-strand	105-106	2	14
β-strand	110-113	4	14
β-strand	119	1	16
α-helix	120-121	2
β-strand	122-126	5	17
α-helix	127-129	3
α-helix	130-134	5
β-strand	137-147	11	17
β-strand	148	1	16
β-strand	153-158	6	18
β-strand	162-163	2	18
β-strand	167-171	5	17
α-helix	172-175	4
β-strand	181-190	10	17
α-helix	191-195	5
β-strand	199-205	7	18
β-strand	213-218	6	18

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-99	8	14
α-helix	106-107	2
β-strand	111-114	4	14
β-strand	118-120	3	14
β-strand	121-122	2	20
α-helix	125-127	3
β-strand	128	1	21
α-helix	129-130	2
β-strand	131-135	5	22
β-strand	146-156	11	22
β-strand	157	1	21
β-strand	162-165	4	23
α-helix	166-168	3
β-strand	170	1	23
β-strand	174-176	3	22
α-helix	177-179	3
β-strand	180-181	2	22
β-strand	187-196	10	22
α-helix	197-201	5
β-strand	205-211	7	23
α-helix	212-214	3
β-strand	216-222	7	23

Chain F: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	30
β-strand	11-12	2	31
β-strand	18-25	8	30
α-helix	29-31	3
β-strand	34-39	6	25
β-strand	45-51	7	25
β-strand	58-60	3	25
β-strand	68-73	6	30
β-strand	78-83	6	30
α-helix	88-90	3
β-strand	92-99	8	25
α-helix	101-102	2
β-strand	111-114	4	25
β-strand	118-120	3	25
β-strand	121-122	2	31
α-helix	125-127	3
β-strand	128	1	32
β-strand	131-135	5	33
β-strand	146-156	11	33
β-strand	157	1	32
β-strand	162-165	4	34
α-helix	166-168	3
β-strand	170	1	34
β-strand	174-176	3	33
α-helix	177-179	3
β-strand	180-181	2	33
β-strand	187-196	10	33
α-helix	197-201	5
β-strand	205-210	6	34
β-strand	218-222	5	34

Chain G: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-13	4	36
β-strand	19-25	7	35
β-strand	30-31	2	37
α-helix	37	1
β-strand	38-39	2	37
β-strand	41-46	6	36
α-helix	51-52	2
β-strand	53-57	5	36
β-strand	61-62	2	36
α-helix	63	1
β-strand	70-75	6	35
β-strand	78-83	6	35
α-helix	88-90	3
β-strand	92-98	7	36
α-helix	104	1
β-strand	105-106	2	36
β-strand	110-114	5	36
β-strand	119	1	38
α-helix	120-121	2
β-strand	122-126	5	39
α-helix	127-129	3
α-helix	130-134	5
β-strand	137-147	11	39
β-strand	148	1	38
β-strand	153-158	6	40
β-strand	161-163	3	40
β-strand	167-171	5	39
α-helix	172-175	4
β-strand	181-190	10	39
α-helix	191-195	5
β-strand	199-205	7	40
β-strand	213-218	6	40

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	41
β-strand	11-12	2	42
β-strand	18-25	8	41
α-helix	29-31	3
β-strand	34-39	6	43
β-strand	45-51	7	43
β-strand	58-60	3	43
β-strand	68-73	6	41
β-strand	78-83	6	41
α-helix	88-90	3
β-strand	92-99	8	43
α-helix	105-107	3
β-strand	111-114	4	43
β-strand	118-120	3	43
β-strand	121-122	2	42
α-helix	125-127	3
β-strand	128	1	44
α-helix	129-130	2
β-strand	131-135	5	45
β-strand	146-156	11	45
β-strand	157	1	44
β-strand	162-165	4	46
α-helix	166-168	3
β-strand	170	1	46
β-strand	174-176	3	45
α-helix	177-179	3
β-strand	180	1	47
β-strand	187	1	45
β-strand	188	1	47
β-strand	189-196	8	45
α-helix	197-201	5
β-strand	205-211	7	46
β-strand	216-222	7	46

Chain Q: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	90-93	4	48
β-strand	99-103	5	48
β-strand	106-113	8	48
β-strand	124-126	3	48
α-helix	129-132	4
α-helix	142-152	11
α-helix	160-161	2
β-strand	162-164	3	48
β-strand	175-178	4	48
α-helix	187-199	13
β-strand	214-219	6	48
α-helix	223-229	7

3 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
CR1-07 Fab light chain	A, C, E, G	protein	221	Homo sapiens	Q0KKI6 (AlphaFold model)
CR1-07 Fab heavy chain	B, D, F, H	protein	226	Homo sapiens	Q6N089 (AlphaFold model)
Pre-glycoprotein polyprotein GP complex	Q, R, S, T	protein	152	Machupo virus	Q8AZ57 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5W1M_1 CR1-07 Fab light chain (chains A, C, E, G)
DIVMTQSPESLAVSLGERATINCKSSQSVLYSSRSDNKDYLAWYQQKPGQSPKLLIYWAS
TRESGVPERFTGSGSGTDFTLSISSLQAEDVAVYYCQQYYSSPPTFGGGTKVELKRTVAA
PSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDST
YSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (B, D, F, H), FASTA

>5W1M_2 CR1-07 Fab heavy chain (chains B, D, F, H)
VQLVESGGGVVHPGRSLRLSCAASGFTFGTSIMHWVRQAPGKGMQWVAQISHDESRKFYS
DSVKGRFTVSRDNSKNTLFLEMSSLRIEDTAVYYCAKDLSPPYSYAWDIFQYWGQGSLVT
VSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 3 (Q, R, S, T), FASTA

>5W1M_3 Pre-glycoprotein polyprotein GP complex (chains Q, R, S, T)
ELPSLCMLNNSFYYMRGGVNTFLIRVSDISVLMKEYDVSIYEPEDLGNCLNKSDSSWAIH
WFSNALGHDWLMDPPMLCRNKTKKEGSNIQFNISKADDARVYGKKIRNGMRHLFRGFHDP
CEEGKVCYLTINQCGDPSSFDYCGVNHLSKCQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
BMA	beta-D-mannopyranose	C6 H12 O6	1

Primary citation

Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses. Clark, L.E., Mahmutovic, S., Raymond, D.D. et al. Nat Commun (2018) 9:1884-1884. DOI 10.1038/s41467-018-04271-z · PubMed

Other PDB entries of the same protein (UniProt Q0KKI6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LKX 1.92 Å, Humanized antibody 4B12 Fab complexed with a CemX segment
5VZY 2.32 Å, Crystal structure of crenezumab Fab in complex with Abeta
5VZX 2.5 Å, Crystal structure of crenezumab Fab

Browse structure collections

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