[English] 日本語
Yorodumi
- PDB-7rku: Structure of the SARS-CoV-2 receptor binding domain in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rku
TitleStructure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022
Components
  • C022 Antibody Fab Heavy Chain
  • C022 Antibody Fab Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Surface protein / Fab / coronavirus / fusion protein / binding domain / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, 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: 3.2 Å
AuthorsJette, C.A. / Bjorkman, P.J. / Barnes, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
CitationJournal: Cell Rep / Year: 2021
Title: Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Authors: Claudia A Jette / Alexander A Cohen / Priyanthi N P Gnanapragasam / Frauke Muecksch / Yu E Lee / Kathryn E Huey-Tubman / Fabian Schmidt / Theodora Hatziioannou / Paul D Bieniasz / Michel C ...Authors: Claudia A Jette / Alexander A Cohen / Priyanthi N P Gnanapragasam / Frauke Muecksch / Yu E Lee / Kathryn E Huey-Tubman / Fabian Schmidt / Theodora Hatziioannou / Paul D Bieniasz / Michel C Nussenzweig / Anthony P West / Jennifer R Keeffe / Pamela J Bjorkman / Christopher O Barnes /
Abstract: Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding ...Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD β sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 13, 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 / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: Spike protein S1
D: Spike protein S1
E: C022 Antibody Fab Heavy Chain
F: C022 Antibody Fab Light Chain
G: C022 Antibody Fab Heavy Chain
H: C022 Antibody Fab Heavy Chain
I: C022 Antibody Fab Light Chain
J: C022 Antibody Fab Heavy Chain
K: C022 Antibody Fab Light Chain
L: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,99216
Polymers294,37612
Non-polymers1,6164
Water00
1
A: Spike protein S1
G: C022 Antibody Fab Heavy Chain
I: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1814
Polymers73,5943
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
J: C022 Antibody Fab Heavy Chain
K: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1814
Polymers73,5943
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spike protein S1
H: C022 Antibody Fab Heavy Chain
L: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8154
Polymers73,5943
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Spike protein S1
E: C022 Antibody Fab Heavy Chain
F: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8154
Polymers73,5943
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.385, 178.385, 247.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 334 through 527)
d_2ens_1(chain "B" and resid 334 through 527)
d_3ens_1(chain "C" and resid 334 through 527)
d_4ens_1(chain "D" and resid 334 through 527)
d_1ens_2(chain "E" and (resid 1 through 20 or (resid 21...
d_2ens_2(chain "G" and (resid 1 through 20 or (resid 21...
d_3ens_2(chain "H" and (resid 1 through 126 or resid 133 through 229))
d_4ens_2(chain "J" and (resid 1 through 20 or (resid 21...
d_1ens_3(chain "F" and (resid 1 through 9 or (resid 10...
d_2ens_3(chain "I" and (resid 1 through 9 or (resid 10...
d_3ens_3(chain "K" and (resid 1 through 146 or resid 148 through 177 or resid 179 through 197))
d_4ens_3(chain "L" and (resid 1 through 9 or (resid 10...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNPROA2 - 195
d_21ens_1ASNPROE2 - 195
d_31ens_1ASNPROI1 - 194
d_41ens_1ASNPROK1 - 194
d_11ens_2GLNPROM1 - 142
d_12ens_2GLYPROM149 - 229
d_21ens_2GLNPROO1 - 223
d_31ens_2GLNPROP1 - 142
d_32ens_2GLYPROP149 - 229
d_41ens_2GLNPROJ1 - 142
d_42ens_2GLYPROJ144 - 224
d_11ens_3ASPSERN1 - 162
d_12ens_3THRALAN164 - 193
d_13ens_3GLUGLUN195 - 213
d_21ens_3ASPSERI1 - 162
d_22ens_3THRALAI164 - 193
d_23ens_3GLUGLUI195 - 213
d_31ens_3ASPSERK1 - 162
d_32ens_3THRALAK164 - 193
d_33ens_3GLUGLUK195 - 213
d_41ens_3ASPSERL1 - 162
d_42ens_3THRALAL164 - 193
d_43ens_3GLUGLUL195 - 213

NCS ensembles :
ID
ens_1
ens_2
ens_3

-
Components

#1: Protein
Spike protein S1


Mass: 24004.926 Da / Num. of mol.: 4 / Fragment: Receptor Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody
C022 Antibody Fab Heavy Chain


Mass: 25978.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody
C022 Antibody Fab Light Chain


Mass: 23610.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#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.: 2
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: 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.: 2 / 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
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.05M ammonium sulfate, 0.05M BIS-Tris, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→44.6 Å / Num. obs: 73262 / % possible obs: 99.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 125.06 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.87
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 7338 / CC1/2: 0.277 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Coot0.8.9.1model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K8M

7k8m


Resolution: 3.2→44.6 Å / SU ML: 0.511 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 3595 4.93 %
Rwork0.1876 69365 -
obs0.1898 72960 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.39 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19668 0 106 0 19774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01120324
X-RAY DIFFRACTIONf_angle_d1.282227686
X-RAY DIFFRACTIONf_chiral_restr0.06493067
X-RAY DIFFRACTIONf_plane_restr0.00963533
X-RAY DIFFRACTIONf_dihedral_angle_d14.50377240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.410639754073
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.929440084188
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.976753780576
ens_2d_2MX-RAY DIFFRACTIONTorsion NCS4.5671602254
ens_2d_3MX-RAY DIFFRACTIONTorsion NCS0.437744752325
ens_2d_4MX-RAY DIFFRACTIONTorsion NCS4.58605167867
ens_3d_2NX-RAY DIFFRACTIONTorsion NCS4.10929182106
ens_3d_3NX-RAY DIFFRACTIONTorsion NCS4.1040228587
ens_3d_4NX-RAY DIFFRACTIONTorsion NCS0.47729285631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.36891220.36212534X-RAY DIFFRACTION93.55
3.24-3.290.34941180.32362631X-RAY DIFFRACTION98.85
3.29-3.330.36171340.33952644X-RAY DIFFRACTION99.32
3.33-3.380.3641100.33592694X-RAY DIFFRACTION99.89
3.38-3.440.38891830.31122664X-RAY DIFFRACTION99.93
3.44-3.490.36491170.29592677X-RAY DIFFRACTION100
3.49-3.550.31161300.28052699X-RAY DIFFRACTION99.93
3.55-3.620.35981390.25242644X-RAY DIFFRACTION100
3.62-3.690.3151270.23732687X-RAY DIFFRACTION99.96
3.69-3.760.29271530.24472673X-RAY DIFFRACTION99.96
3.76-3.840.25311390.23112645X-RAY DIFFRACTION99.93
3.84-3.930.28771400.22132681X-RAY DIFFRACTION99.96
3.93-4.030.24671330.20882685X-RAY DIFFRACTION100
4.03-4.140.23881230.2192700X-RAY DIFFRACTION100
4.14-4.260.27021470.18472664X-RAY DIFFRACTION100
4.26-4.40.21991430.16692649X-RAY DIFFRACTION99.96
4.4-4.560.18721240.15062707X-RAY DIFFRACTION100
4.56-4.740.1651520.14442647X-RAY DIFFRACTION99.96
4.74-4.950.16251450.15332710X-RAY DIFFRACTION100
4.95-5.220.22591330.16042650X-RAY DIFFRACTION99.96
5.22-5.540.19761530.16432687X-RAY DIFFRACTION100
5.54-5.970.21991420.16142680X-RAY DIFFRACTION100
5.97-6.570.24471780.18742644X-RAY DIFFRACTION100
6.57-7.510.25871260.18092706X-RAY DIFFRACTION99.96
7.52-9.450.18771400.1512698X-RAY DIFFRACTION99.96
9.45-44.60.19291440.16272665X-RAY DIFFRACTION98.05

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more