5W1K: JUNV GP1 CR1-10 Fab CR1-28 Fab complex

JUNV GP1 CR1-10 Fab CR1-28 Fab complex. Determined by X-ray diffraction at 3.99 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 3.99 Å
Organisms: Homo sapiens, Junin mammarenavirus
Chains: 20
Atoms: 31,130
Mol. weight: 443.01 kDa
Ligands: NAG
Released: 30 May 2018

Explore 5W1K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W1K contains 105 α-helices and 398 β-strands across 20 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-12	3	2
β-strand	19-25	7	1
β-strand	34-38	5	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-87	3	3
β-strand	98-100	3	2
β-strand	109-113	5	4
α-helix	114-116	3
α-helix	117-121	5
β-strand	124-134	11	4
β-strand	140-145	6	5
α-helix	152-154	3
β-strand	156-159	4	4
β-strand	168-177	10	4
α-helix	178-181	4
β-strand	187-192	6	5
β-strand	201-204	4	5

Chain B: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	12	1	7
β-strand	18-25	8	6
β-strand	34	1	8
β-strand	35-40	6	9
β-strand	44-47	4	9
β-strand	49	1	10
β-strand	51	1	8
β-strand	60	1	10
β-strand	69-73	5	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-97	6	9
β-strand	102	1	11
β-strand	105-106	2	11
β-strand	120-122	3	9
β-strand	124	1	7
α-helix	127-129	3
β-strand	130	1	12
β-strand	133-137	5	13
β-strand	150-158	9	13
β-strand	159	1	12
β-strand	164-167	4	14
β-strand	177-178	2	13
α-helix	179-181	3
β-strand	182-183	2	13
β-strand	189-196	8	13
α-helix	199-201	3
β-strand	207-213	7	14
β-strand	218-224	7	14

Chain C: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
β-strand	19-25	7	15
β-strand	29	1	17
α-helix	31-33	3
β-strand	35-39	5	16
β-strand	46-47	2	16
β-strand	49-50	2	18
β-strand	54-55	2	18
α-helix	56	1
β-strand	63-68	6	15
β-strand	69	1	17
β-strand	71-76	6	15
α-helix	81-83	3
β-strand	85-92	8	16
β-strand	97-99	3	16
α-helix	100	1
β-strand	103-107	5	16
α-helix	112-114	3
β-strand	115-119	5	19
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	19
β-strand	146-151	6	20
β-strand	155	1	20
β-strand	161-164	4	19
β-strand	168	1	21
β-strand	173	1	21
β-strand	174-183	10	19
α-helix	184-188	5
β-strand	192-198	7	20
β-strand	207-211	5	20

Chain D: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	11-12	2	23
β-strand	18-24	7	22
β-strand	36-41	6	24
β-strand	47-53	7	24
β-strand	61	1	24
β-strand	69-70	2	22
β-strand	73-74	2	22
β-strand	79-84	6	22
α-helix	89-91	3
β-strand	93-99	7	24
β-strand	120-122	3	24
β-strand	123-124	2	23
α-helix	128-129	2
β-strand	130	1	25
β-strand	133-137	5	26
β-strand	144-145	2	27
β-strand	148-149	2	27
β-strand	151-158	8	26
β-strand	159	1	25
β-strand	164-167	4	28
β-strand	176-178	3	26
α-helix	179-181	3
β-strand	182-183	2	26
β-strand	189-195	7	26
β-strand	198	1	27
α-helix	199-201	3
β-strand	207-213	7	28
β-strand	218-224	7	28

Chain E: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	90-94	5	29
β-strand	98-103	6	29
β-strand	106-113	8	29
β-strand	124-126	3	29
α-helix	132-134	3
α-helix	139-151	13
α-helix	160-161	2
β-strand	162-164	3	29
β-strand	175-178	4	29
α-helix	183-185	3
α-helix	186-199	14
β-strand	214-219	6	29
α-helix	221-223	3

Chain F: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	10-12	3	31
β-strand	19-25	7	30
β-strand	34-38	5	31
β-strand	45-49	5	31
β-strand	53-54	2	31
α-helix	55	1
β-strand	62-67	6	30
β-strand	70-75	6	30
α-helix	80-82	3
β-strand	85-87	3	31
β-strand	97-100	4	31
β-strand	109-113	5	32
α-helix	114-116	3
α-helix	117-121	5
β-strand	124	1	33
β-strand	127-134	8	32
β-strand	140-145	6	34
α-helix	152-154	3
β-strand	156-159	4	32
β-strand	168-174	7	32
β-strand	177	1	33
α-helix	178-181	4
β-strand	187-192	6	34
β-strand	201-204	4	34

Chain G: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	35
β-strand	12	1	36
β-strand	18-25	8	35
α-helix	33-34	2
β-strand	35-40	6	37
β-strand	44-51	8	37
β-strand	57-60	4	37
β-strand	69-73	5	35
β-strand	78-83	6	35
α-helix	88-90	3
β-strand	92-97	6	37
β-strand	120-122	3	37
β-strand	124	1	36
β-strand	130	1	38
β-strand	133-137	5	39
β-strand	150-158	9	39
β-strand	159	1	38
β-strand	164-167	4	40
β-strand	177-178	2	39
α-helix	179-181	3
β-strand	182-183	2	39
β-strand	189-196	8	39
α-helix	199-201	3
β-strand	207-213	7	40
β-strand	218-224	7	40

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	10-13	4	42
β-strand	19-25	7	41
β-strand	35-39	5	42
β-strand	46-50	5	42
β-strand	54-55	2	42
α-helix	56	1
β-strand	63-68	6	41
β-strand	71-76	6	41
α-helix	81-83	3
β-strand	86-92	7	42
β-strand	97-99	3	42
β-strand	103-107	5	42
β-strand	112	1	43
α-helix	113-114	2
β-strand	115-119	5	44
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	44
β-strand	141	1	43
β-strand	146-151	6	45
β-strand	155	1	45
β-strand	161-164	4	44
β-strand	168	1	46
β-strand	173	1	46
β-strand	174-183	10	44
α-helix	184-188	5
β-strand	192-198	7	45
β-strand	207-211	5	45

12 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
CR1-28 Fab light chain	A, F, K, S	protein	206	Homo sapiens	P0DOX7 (AlphaFold model)
CR1-28 Fab heavy chain	B, G, L, T	protein	226	Homo sapiens	S6C4R2 (AlphaFold model)
CR1-10 Fab light chain	C, H, M, N	protein	213	Homo sapiens	Q6PIL8 (AlphaFold model)
CR1-10 Fab heavy chain	D, I, O, Q	protein	225	Homo sapiens	S6B2B6 (AlphaFold model)
Pre-glycoprotein polyprotein GP complex	E, J, P, R	protein	142	Junin mammarenavirus	P26313

Sequence of entity 1 (A, F, K, S), FASTA

>5W1K_1 CR1-28 Fab light chain (chains A, F, K, S)
IQMTQSPSTLSASVGDRVTITCRASQSIDNWLAWYQQKPGKAPKLLIYTASRLESGVPSR
FSGSGSGTEFTLTISSLQPDDFATYYCQHRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLK
SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY
EKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 2 (B, G, L, T), FASTA

>5W1K_2 CR1-28 Fab heavy chain (chains B, G, L, T)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSSAMHWVRQAPGKGLEWVAVIWSDGSNENY
ADSVKGRFTISRDNSKNTLYLQMSSLRAEDTAVYYCATDKTYVSGYTSTWYYFNYWGQGT
LVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP

Sequence of entity 3 (C, H, M, N), FASTA

>5W1K_3 CR1-10 Fab light chain (chains C, H, M, N)
IVLTQSPGTLSLSPGETATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASGRATGIPD
RFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGRSGYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 4 (D, I, O, Q), FASTA

>5W1K_4 CR1-10 Fab heavy chain (chains D, I, O, Q)
VQLQESGPGLVKPSQTLSLTCSVSGGSIGGSSYYWSWIRHHPGKGLEWIGYINYRGITHY
NAALKSRVSMSVETSQNHFSLQLTSVTAADTAVYYCARLTSDCSGGNCYQAFDYWGQGSL
VSVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP

Sequence of entity 5 (E, J, P, R), FASTA

>5W1K_5 Pre-glycoprotein polyprotein GP complex (chains E, J, P, R)
DLPLLCTLNKSHLYIKGGNASFKISFDDIAVLLPEYDVIIQHPADMSWCSKSDDQIWLSQ
WFMNAVGHDWYLDPPFLCRNRTKTEGFIFQVNTSKTGINENYAKKFKTGMHHLYREYPDS
CLDGKLCLMKAQPTSWPLQCPL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N 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 P0DOX7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6MU3 2.33 Å, Anti-HIV-1 Fab 2G12 + Man7 re-refinement
6MUB 2.5 Å, Anti-HIV-1 Fab 2G12 + Man5 re-refinement
8BBO 2.75 Å, SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab
2R56 2.8 Å, Crystal Structure of a Recombinant IgE Fab Fragment in Complex with Bovine…
6UTE 2.9 Å, Crystal structure of Z032 Fab in complex with WNV EDIII
5VIC 3.0 Å, Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII
5VIG 3.0 Å, Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII
6UTA 3.1 Å, Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII
2QAD 3.3 Å, Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4
4XI5 3.9 Å, gHgL of varicella-zoster virus in complex with human neutralizing antibodies

Browse structure collections

About this viewer

MolViewer shows 5W1K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.