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- PDB-7mzh: SARS-CoV-2 receptor binding domain bound to Fab WCSL 119 -

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Basic information

Entry
Database: PDB / ID: 7mzh
TitleSARS-CoV-2 receptor binding domain bound to Fab WCSL 119
Components
  • Spike protein S1
  • WCSL 119 heavy chain
  • WCSL 119 light chain
KeywordsVIRAL PROTEIN / SARS-CoV-2 / spike / RBD / human antibody
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPymm, P. / Tan, L.L. / Dietrich, M.H. / Chan, L.J. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT2002073 Australia
CitationJournal: Cell Rep / Year: 2021
Title: Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain.
Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon- ...Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon-Xhi Tan / Jennifer A Juno / Kathleen M Wragg / Thakshila Amarasena / Ester Lopez / Kevin J Selva / Ebene R Haycroft / James P Cooney / Hariprasad Venugopal / Li Lynn Tan / Matthew T O Neill / Cody C Allison / Deborah Cromer / Miles P Davenport / Richard A Bowen / Amy W Chung / Marc Pellegrini / Mark T Liddament / Alisa Glukhova / Kanta Subbarao / Stephen J Kent / Wai-Hong Tham /
Abstract: Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike ...Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike protein can exhibit neutralization resistance, potentially affecting the effectiveness of some antibody-based therapeutics. Here, the generation of a diverse panel of 91 human, neutralizing monoclonal antibodies provides an in-depth structural and phenotypic definition of receptor binding domain (RBD) antigenic sites on the viral spike. These RBD antibodies ameliorate SARS-CoV-2 infection in mice and hamster models in a dose-dependent manner and in proportion to in vitro, neutralizing potency. Assessing the effect of mutations in the spike protein on antibody recognition and neutralization highlights both potent single antibodies and stereotypic classes of antibodies that are unaffected by currently circulating VOCs, such as B.1.351 and P.1. These neutralizing monoclonal antibodies and others that bind analogous epitopes represent potentially useful future anti-SARS-CoV-2 therapeutics.
History
DepositionMay 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 27, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Spike protein S1
H: WCSL 119 heavy chain
L: WCSL 119 light chain
A: Spike protein S1
B: WCSL 119 heavy chain
C: WCSL 119 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,1038
Polymers139,6226
Non-polymers1,4812
Water4,071226
1
E: Spike protein S1
H: WCSL 119 heavy chain
L: WCSL 119 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3974
Polymers69,8113
Non-polymers5871
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-31 kcal/mol
Surface area28360 Å2
MethodPISA
2
A: Spike protein S1
B: WCSL 119 heavy chain
C: WCSL 119 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7064
Polymers69,8113
Non-polymers8951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-19 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.704, 72.833, 103.988
Angle α, β, γ (deg.)90.000, 90.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 333 through 345 or (resid 346...
21(chain E and (resid 333 through 334 or (resid 335...
12(chain B and (resid 1 through 122 or (resid 123...
22(chain H and ((resid 1 and (name N or name...
13(chain C and (resid 2 through 126 or resid 128...
23(chain L and (resid 2 through 42 or (resid 43...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRTHRTHR(chain A and (resid 333 through 345 or (resid 346...AD333 - 3453 - 15
121ARGARGARGARG(chain A and (resid 333 through 345 or (resid 346...AD34616
211THRTHRASNASN(chain E and (resid 333 through 334 or (resid 335...EA333 - 3343 - 4
221LEULEULEULEU(chain E and (resid 333 through 334 or (resid 335...EA3355
112GLUGLUVALVAL(chain B and (resid 1 through 122 or (resid 123...BE1 - 1221 - 122
122PHEPHEPHEPHE(chain B and (resid 1 through 122 or (resid 123...BE123123
132GLUGLUSERSER(chain B and (resid 1 through 122 or (resid 123...BE1 - 2161 - 216
142GLUGLUSERSER(chain B and (resid 1 through 122 or (resid 123...BE1 - 2161 - 216
152GLUGLUSERSER(chain B and (resid 1 through 122 or (resid 123...BE1 - 2161 - 216
162GLUGLUSERSER(chain B and (resid 1 through 122 or (resid 123...BE1 - 2161 - 216
212GLUGLUGLUGLU(chain H and ((resid 1 and (name N or name...HB11
222GLUGLUCYSCYS(chain H and ((resid 1 and (name N or name...HB1 - 2171 - 217
232GLUGLUCYSCYS(chain H and ((resid 1 and (name N or name...HB1 - 2171 - 217
242GLUGLUCYSCYS(chain H and ((resid 1 and (name N or name...HB1 - 2171 - 217
252GLUGLUCYSCYS(chain H and ((resid 1 and (name N or name...HB1 - 2171 - 217
113SERSERSERSER(chain C and (resid 2 through 126 or resid 128...CF2 - 1262 - 126
123GLUGLUHISHIS(chain C and (resid 2 through 126 or resid 128...CF128 - 192128 - 192
133ARGARGARGARG(chain C and (resid 2 through 126 or resid 128...CF193193
143GLNGLNSERSER(chain C and (resid 2 through 126 or resid 128...CF1 - 2161 - 216
153GLNGLNSERSER(chain C and (resid 2 through 126 or resid 128...CF1 - 2161 - 216
163GLNGLNSERSER(chain C and (resid 2 through 126 or resid 128...CF1 - 2161 - 216
173GLNGLNSERSER(chain C and (resid 2 through 126 or resid 128...CF1 - 2161 - 216
213SERSERGLYGLY(chain L and (resid 2 through 42 or (resid 43...LC2 - 422 - 42
223LYSLYSLYSLYS(chain L and (resid 2 through 42 or (resid 43...LC4343
233SERSERCYSCYS(chain L and (resid 2 through 42 or (resid 43...LC2 - 2152 - 215
243SERSERCYSCYS(chain L and (resid 2 through 42 or (resid 43...LC2 - 2152 - 215
253SERSERCYSCYS(chain L and (resid 2 through 42 or (resid 43...LC2 - 2152 - 215
263SERSERCYSCYS(chain L and (resid 2 through 42 or (resid 43...LC2 - 2152 - 215
273SERSERCYSCYS(chain L and (resid 2 through 42 or (resid 43...LC2 - 2152 - 215

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules HBLC

#2: Antibody WCSL 119 heavy chain


Mass: 23769.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody WCSL 119 light chain


Mass: 22967.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 228 molecules EA

#1: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain (RBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14% PEG3350, 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.1→46.85 Å / Num. obs: 81929 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / Net I/σ(I): 11.8 / Num. measured all: 416245 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.144.90.822204845260.8050.4110.921.899.9
10.91-46.854.70.02529836310.9990.0130.02939.998.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 2.1→45.701 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 3922 4.8 %
Rwork0.2199 77866 -
obs0.2221 81788 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.25 Å2 / Biso mean: 49.4551 Å2 / Biso min: 29.83 Å2
Refinement stepCycle: final / Resolution: 2.1→45.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9450 0 99 226 9775
Biso mean--81.65 45.54 -
Num. residues----1256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1232X-RAY DIFFRACTION5.493TORSIONAL
12E1232X-RAY DIFFRACTION5.493TORSIONAL
21B1238X-RAY DIFFRACTION5.493TORSIONAL
22H1238X-RAY DIFFRACTION5.493TORSIONAL
31C1272X-RAY DIFFRACTION5.493TORSIONAL
32L1272X-RAY DIFFRACTION5.493TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12560.45411500.34842774100
2.1256-2.15250.3771480.34342743100
2.1525-2.18080.38281510.33362784100
2.1808-2.21070.3871260.32152773100
2.2107-2.24230.36761480.31592721100
2.2423-2.27580.34911590.30452779100
2.2758-2.31130.33541340.28532747100
2.3113-2.34920.31511010.29482797100
2.3492-2.38970.3271680.27852718100
2.3897-2.43320.27461100.26842803100
2.4332-2.480.31091440.26082806100
2.48-2.53060.31621410.2562753100
2.5306-2.58560.34421200.26322773100
2.5856-2.64570.35541310.2489277699
2.6457-2.71190.27041630.2472755100
2.7119-2.78520.34641350.24982761100
2.7852-2.86720.31041230.2555277299
2.8672-2.95970.33061370.24932805100
2.9597-3.06550.2781310.24012778100
3.0655-3.18820.28051380.242793100
3.1882-3.33320.23731470.23652794100
3.3332-3.50890.32441470.23682753100
3.5089-3.72860.29011360.22432826100
3.7286-4.01640.24521440.20152775100
4.0164-4.42030.24471730.16962767100
4.4203-5.05920.1941350.15792812100
5.0592-6.37130.19251290.17492844100
6.3713-45.7010.16481530.1634288499

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