6W41: SARS-CoV-2 receptor binding domain

Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022. Determined by X-ray diffraction at 3.08 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 3.08 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 4,936
Mol. weight: 74.43 kDa
Ligands: NAG
Released: 25 Mar 2020

Explore 6W41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W41 contains 20 α-helices and 61 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 C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	334-335	2	12
α-helix	338-342	5
β-strand	354-358	5	13
β-strand	361-362	2	12
α-helix	366-370	5
β-strand	376-379	4	13
β-strand	391-392	2	12
β-strand	394-403	10	13
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	13
β-strand	448	1	14
β-strand	452-454	3	15
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	16
β-strand	485	1	16
β-strand	488-489	2	16
β-strand	492-494	3	15
β-strand	497	1	14
α-helix	503-505	3
β-strand	507-516	10	13
α-helix	521-522	2
β-strand	524-525	2	12

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	33-39	7	2
β-strand	45-52	8	2
β-strand	56-59	4	2
β-strand	68-72	5	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	117	1	3
β-strand	120-124	5	4
α-helix	125-127	3
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	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	186-189	4
β-strand	194-200	7	5
β-strand	205-211	7	5

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	27D	1	8
β-strand	30	1	8
β-strand	33-38	6	7
α-helix	43-44	2
β-strand	45-49	5	7
β-strand	53-54	2	7
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-155	3	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CR3022 Fab heavy chain	H	protein	222	Homo sapiens
CR3022 Fab light chain	L	protein	221	Homo sapiens
Spike protein S1	C	protein	231	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6W41_1 CR3022 Fab heavy chain (chains H)
QMQLVQSGTEVKKPGESLKISCKGSGYGFITYWIGWVRQMPGKGLEWMGIIYPGDSETRY
SPSFQGQVTISADKSINTAYLQWSSLKASDTAIYYCAGGSGISTPMDVWGQGTTVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>6W41_2 CR3022 Fab light chain (chains L)
DIQLTQSPDSLAVSLGERATINCKSSQSVLYSSINKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPYTFGQGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Sequence of entity 3 (C), FASTA

>6W41_3 Spike protein S1 (chains C)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQ
PTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH

Ligands and cofactors

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

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Yuan, M., Wu, N.C., Zhu, X. et al. Science (2020) 368:630-633. DOI 10.1126/science.abb7269 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…

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6W41 is part of these collections:

SARS-CoV-2 and COVID-19

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