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- PDB-7jmp: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7jmp
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39
Components
  • COVA2-39 heavy chain
  • COVA2-39 light chain
  • Spike protein S1
KeywordsViral Protein/IMMUNE SYSTEM / SARS-CoV-2 / COVID-19 / RBD / Antibody / SARS / Spike / IMMUNE SYSTEM / Viral Protein-IMMUNE SYSTEM complex
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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 Å
AuthorsWu, N.C. / Yuan, M. / Liu, H. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
Bill & Melinda Gates FoundationOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657
CitationJournal: Cell Rep / Year: 2020
Title: An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.
Authors: Wu, N.C. / Yuan, M. / Liu, H. / Lee, C.D. / Zhu, X. / Bangaru, S. / Torres, J.L. / Caniels, T.G. / Brouwer, P.J.M. / van Gils, M.J. / Sanders, R.W. / Ward, A.B. / Wilson, I.A.
History
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: COVA2-39 heavy chain
L: COVA2-39 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7764
Polymers73,5553
Non-polymers2211
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-29 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.905, 80.445, 72.006
Angle α, β, γ (deg.)90.000, 104.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody COVA2-39 heavy chain


Mass: 24710.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody COVA2-39 light chain


Mass: 22749.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 5.6 20% isopropanol 10% ethylene glycol 20% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.712→50 Å / Num. obs: 79139 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / Χ2: 1.326 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.753.50.93439200.5060.5761.1030.46397.6
1.75-1.783.60.70339590.6840.4270.8270.41998
1.78-1.823.60.58539690.740.3510.6860.43798.1
1.82-1.853.60.4439750.8370.2620.5140.44298.5
1.85-1.893.60.36640080.8520.2190.4290.57798.1
1.89-1.943.40.33539210.8490.2120.3990.88996.4
1.94-1.993.60.22439530.9360.1360.2640.63398
1.99-2.043.60.17339970.9670.1050.2030.63197.5
2.04-2.13.30.15838630.9640.10.1880.9395.5
2.1-2.173.20.10937830.9830.0690.130.7992.8
2.17-2.243.70.10839130.9860.0630.1250.8997.2
2.24-2.333.60.11139510.9790.0670.1311.42997.2
2.33-2.4440.08339810.9910.0470.0961.16397.9
2.44-2.573.90.07639830.990.0440.0881.44397.4
2.57-2.733.80.06839660.9930.0390.0791.80797.7
2.73-2.943.70.05839580.9950.0340.0682.20296.9
2.94-3.243.50.04938540.9960.0290.0582.58694.5
3.24-3.7140.04540710.9970.0250.0512.90399.4
3.71-4.6740.0440550.9980.0210.0452.7998.5
4.67-503.80.03440590.9980.0180.0392.25996.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 1.712→34.824 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 3841 4.86 %
Rwork0.1768 75260 -
obs0.1783 79101 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.37 Å2 / Biso mean: 34.7183 Å2 / Biso min: 15.6 Å2
Refinement stepCycle: final / Resolution: 1.712→34.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 14 482 4926
Biso mean--84.38 42.25 -
Num. residues----594
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.712-1.73320.3261240.3088235582
1.7332-1.7560.30961430.2742283498
1.756-1.780.29621520.2486278698
1.78-1.80550.25061690.2308281498
1.8055-1.83240.2561690.2126281998
1.8324-1.8610.25541340.2009284398
1.861-1.89160.23021510.2149276098
1.8916-1.92420.26751560.2333275096
1.9242-1.95920.26031510.202284198
1.9592-1.99680.21391600.1875279198
1.9968-2.03760.19811340.1793277597
2.0376-2.08190.2221240.1863274995
2.0819-2.13030.20971640.1745266394
2.1303-2.18360.21521650.1746268694
2.1836-2.24260.23411430.1821280597
2.2426-2.30860.23021350.1879281997
2.3086-2.38310.20261490.1834279898
2.3831-2.46820.23151390.1701283398
2.4682-2.5670.18761280.1809281497
2.567-2.68380.2141180.1779282497
2.6838-2.82530.23841400.1828281398
2.8253-3.00220.21751330.1844280395
3.0022-3.23380.23451320.1858271795
3.2338-3.5590.21141330.1699291399
3.559-4.07330.20151020.1584293799
4.0733-5.12930.15481330.1379287698
5.1293-34.8240.17051600.1705284296
Refinement TLS params.Method: refined / Origin x: -37.9424 Å / Origin y: 9.8245 Å / Origin z: 20.2696 Å
111213212223313233
T0.2012 Å20.0024 Å20.0139 Å2-0.1765 Å2-0.0188 Å2--0.1684 Å2
L1.4 °20.0061 °20.1568 °2-0.1974 °2-0.0692 °2--0.49 °2
S-0.0034 Å °0.1973 Å °0.026 Å °-0.0339 Å °-0.0024 Å °0.044 Å °0.0518 Å °-0.0953 Å °0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA338 - 1001
2X-RAY DIFFRACTION1allH2 - 214
3X-RAY DIFFRACTION1allL3 - 209
4X-RAY DIFFRACTION1allS1 - 482

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