5XRQ: Human monoclonal antibody H3v-47

Crystal structure of human monoclonal antibody H3v-47. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,639
Mol. weight: 96.97 kDa
Released: 25 Jul 2018

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

Secondary structure: helices and β-sheets

5XRQ contains 35 α-helices and 88 β-strands across 4 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: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	11
β-strand	11-12	2	12
β-strand	18-23	6	11
α-helix	28-31	4
β-strand	34-40	7	13
β-strand	43-52	10	13
β-strand	56-59	4	13
α-helix	61-63	3
β-strand	67-72	6	11
α-helix	73-75	3
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	100J-103	4	13
β-strand	107-109	3	13
β-strand	110-111	2	12
α-helix	115-116	2
β-strand	117	1	14
β-strand	120-124	5	15
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	16
β-strand	159	1	16
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-185	10	15
α-helix	188-191	4
β-strand	196-200	5	16
β-strand	205-207	3	16

Chain B: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	33-37	5	13
α-helix	43-44	2
β-strand	45-48	4	13
α-helix	53	1
β-strand	54	1	13
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-86	3	18
β-strand	87-90	4	13
β-strand	96-97	2	13
β-strand	101-105	5	18
α-helix	106	1
β-strand	110	1	19
α-helix	111-112	2
β-strand	113-117	5	20
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	20
β-strand	139	1	19
β-strand	144-149	6	21
β-strand	152-153	2	21
β-strand	158-162	5	20
α-helix	163-166	4
β-strand	172-181	10	20
α-helix	182-186	5
β-strand	190-196	7	21
β-strand	205-209	5	21

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-23	6	1
α-helix	27-31	5
β-strand	32-40	9	2
β-strand	44-52	9	2
β-strand	56-59	4	2
α-helix	61-63	3
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	11	2
α-helix	99	1
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	117	1	3
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	150-154	5	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	188-191	4
β-strand	194-200	7	5
β-strand	205-211	7	5

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	6
β-strand	10-13	4	7
α-helix	18	1
β-strand	19-28	11	6
α-helix	30-32	3
β-strand	33-38	6	7
α-helix	43	1
β-strand	44-49	6	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-75	14	6
α-helix	80-82	3
β-strand	84-90	7	7
β-strand	96-97	2	7
β-strand	101-105	5	7
β-strand	110	1	8
β-strand	113-117	5	9
α-helix	121-124	4
β-strand	128-138	11	9
β-strand	139	1	8
β-strand	143-149	7	10
β-strand	152-153	2	10
α-helix	154	1
β-strand	158-159	2	9
β-strand	162-163	2	9
α-helix	164-166	3
β-strand	172-181	10	9
α-helix	182-186	5
β-strand	191-197	7	10
β-strand	204-208	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab H3v-47 heavy chain	A, H	protein	236	Homo sapiens	Q6N089 (AlphaFold model)
Fab H3v-47 light chain	B, L	protein	214	Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>5XRQ_1 Fab H3v-47 heavy chain (chains A, H)
QVQLVQSGAEVKKPGSSVRVSCKASGDTFSSYSITWVRQAPGHGLQWMGGIFPIFGSTNY
AQKFDDRLTITTDDSSRTVYMELTSLRLEDTAVYYCARGASKVEPAAPAYSDAFDMWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Sequence of entity 2 (B, L), FASTA

>5XRQ_2 Fab H3v-47 light chain (chains B, L)
DIVMTQSPGTLSLSPGERATLSCRTSQGVSSSYLAWYQQKPGQAPRLLISGSSSRATGIP
DRFSGSGSGRDFTLTISRLEPEDSAVYYCQQYATSPTFGQGTRVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA. Bangaru, S., Zhang, H., Gilchuk, I.M. et al. Nat Commun (2018) 9:2669-2669. DOI 10.1038/s41467-018-04704-9 · PubMed

Other PDB entries of the same protein (UniProt Q6N089 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HPY 1.5 Å, Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide
5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
3QCU 1.98 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3QCT 2.15 Å, Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab…
3MNV 2.4 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
3QCV 2.51 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
2OQJ 2.8 Å, Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5WKO 3.49 Å, Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1)…

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