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- PDB-7lm9: Crystal structure of SARS-CoV spike protein receptor-binding doma... -

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Basic information

Entry
Database: PDB / ID: 7lm9
TitleCrystal structure of SARS-CoV spike protein receptor-binding domain in complex with a cross-neutralizing antibody CV38-142 Fab isolated from COVID-19 patient
Components
  • (CV38-142 Fab ...) x 2
  • Spike glycoproteinSpike protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV / Antibody / Spike / Coronavirus / SARS / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / Cross-Neutralization / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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 / 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 speciesSARS coronavirus MA15
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsLiu, H. / Yuan, M. / Zhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
Citation
Journal: Cell Host Microbe / Year: 2021
Title: A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.
Authors: Hejun Liu / Meng Yuan / Deli Huang / Sandhya Bangaru / Fangzhu Zhao / Chang-Chun D Lee / Linghang Peng / Shawn Barman / Xueyong Zhu / David Nemazee / Dennis R Burton / Marit J van Gils / ...Authors: Hejun Liu / Meng Yuan / Deli Huang / Sandhya Bangaru / Fangzhu Zhao / Chang-Chun D Lee / Linghang Peng / Shawn Barman / Xueyong Zhu / David Nemazee / Dennis R Burton / Marit J van Gils / Rogier W Sanders / Hans-Christian Kornau / S Momsen Reincke / Harald Prüss / Jakob Kreye / Nicholas C Wu / Andrew B Ward / Ian A Wilson /
Abstract: Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking ...Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.
#1: Journal: Biorxiv / Year: 2021
Title: A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.
Authors: Liu, H. / Yuan, M. / Huang, D. / Bangaru, S. / Lee, C.D. / Peng, L. / Zhu, X. / Nemazee, D. / van Gils, M.J. / Sanders, R.W. / Kornau, H.C. / Reincke, S.M. / Pruss, H. / Kreye, J. / Wu, N.C. ...Authors: Liu, H. / Yuan, M. / Huang, D. / Bangaru, S. / Lee, C.D. / Peng, L. / Zhu, X. / Nemazee, D. / van Gils, M.J. / Sanders, R.W. / Kornau, H.C. / Reincke, S.M. / Pruss, H. / Kreye, J. / Wu, N.C. / Ward, A.B. / Wilson, I.A.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
H: CV38-142 Fab heavy chain
L: CV38-142 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,14914
Polymers73,7963
Non-polymers1,35311
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.997, 71.877, 49.241
Angle α, β, γ (deg.)90.000, 90.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody CV38-142 Fab heavy chain


Mass: 24068.002 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 CV38-142 Fab light chain


Mass: 23745.264 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)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 25982.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus MA15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: D2E265
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 603 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium tartrate, 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.527→50 Å / Num. obs: 120261 / % possible obs: 95.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 1.251 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.563.80.79452410.6470.4190.9050.36984.1
1.56-1.584.90.76457350.7380.3670.8520.38591.1
1.58-1.625.70.71858310.7670.3220.790.39893.8
1.62-1.656.50.69159690.8090.2920.7520.39694.7
1.65-1.686.90.61759090.8610.2530.6680.41395.1
1.68-1.726.90.50559550.9060.2060.5470.4495.3
1.72-1.776.80.39160060.9350.1610.4240.47595.6
1.77-1.816.40.30659870.950.130.3340.53595.7
1.81-1.876.30.24259720.9640.1040.2640.62295.9
1.87-1.936.40.20560440.9720.0870.2230.70996.1
1.93-27.10.17160800.9830.0690.1850.84696.6
2-2.087.10.14560630.9870.0580.1571.02496.6
2.08-2.1770.12860650.9890.0520.1381.1997
2.17-2.296.80.11461110.9890.0470.1231.36197.2
2.29-2.436.50.10361260.990.0430.1121.55797.5
2.43-2.626.10.09161500.990.040.11.8697.8
2.62-2.886.50.08261830.9930.0350.092.24597.9
2.88-3.36.90.07262290.9950.030.0782.80198.4
3.3-4.156.40.06262530.9950.0270.0683.28298.8
4.15-5060.05863520.9950.0260.0643.18498.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMW, 2GHV

7jmw

2ghv


Resolution: 1.53→49.236 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 6011 5 %
Rwork0.1697 114184 -
obs0.1708 120195 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.9 Å2 / Biso mean: 26.9165 Å2 / Biso min: 11.21 Å2
Refinement stepCycle: final / Resolution: 1.53→49.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 114 593 5575
Biso mean--37.35 36.91 -
Num. residues----634
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.53-1.54450.30381590.2684317680
1.5445-1.56270.24981750.2498346587
1.5627-1.58180.28911680.2456367892
1.5818-1.60180.27441560.2312369993
1.6018-1.62290.25022160.2297371395
1.6229-1.64510.23761970.23382795
1.6451-1.66860.2892040.2466371095
1.6686-1.69350.26341940.2159379295
1.6935-1.720.21921970.2082379195
1.72-1.74820.24311920.193383396
1.7482-1.77830.22782000.1778375196
1.7783-1.81070.21831770.1758383196
1.8107-1.84550.20522180.1775379696
1.8455-1.88320.20792220.1738377596
1.8832-1.92410.22252070.1717381796
1.9241-1.96890.17792210.173382996
1.9689-2.01810.20832240.1691379697
2.0181-2.07270.19612290.1656384497
2.0727-2.13370.20872040.1688384697
2.1337-2.20250.19711890.1653385197
2.2025-2.28120.17631890.1613390697
2.2812-2.37260.19412220.167386997
2.3726-2.48060.18321860.1706394198
2.4806-2.61130.19162120.1721387298
2.6113-2.77490.19012310.1699387998
2.7749-2.98920.1832040.1706394298
2.9892-3.28990.21142090.1709395698
3.2899-3.76580.18281930.1632396699
3.7658-4.74390.15151980.1365396098
4.7439-49.2360.15452180.1545407399
Refinement TLS params.Method: refined / Origin x: 47.7987 Å / Origin y: -19.3425 Å / Origin z: -8.1002 Å
111213212223313233
T0.1649 Å20.015 Å2-0.0222 Å2-0.1009 Å20.0009 Å2--0.1015 Å2
L1.7627 °20.2808 °2-0.5938 °2-0.249 °2-0.1266 °2--0.34 °2
S-0.0205 Å °-0.1067 Å °-0.0282 Å °-0.0051 Å °0.0231 Å °0.0224 Å °-0.0025 Å °0.0247 Å °0.0019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA320 - 513
2X-RAY DIFFRACTION1allA1501 - 1504
3X-RAY DIFFRACTION1allH1 - 216
4X-RAY DIFFRACTION1allL1 - 214
5X-RAY DIFFRACTION1allS1 - 10
6X-RAY DIFFRACTION1allW1 - 596

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