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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rks
TitleStructure of the SARS-CoV receptor binding domain in complex with the human neutralizing antibody Fab fragment, C118
Components
  • C118 Antibody Fab Heavy Chain
  • C118 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


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / 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 / 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 / host cell plasma membrane / virion membrane / identical protein binding / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Dec 29, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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
H: C118 Antibody Fab Heavy Chain
I: C118 Antibody Fab Heavy Chain
L: C118 Antibody Fab Light Chain
M: C118 Antibody Fab Light Chain
R: Spike protein S1
S: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5878
Polymers141,5926
Non-polymers9952
Water00
1
H: C118 Antibody Fab Heavy Chain
L: C118 Antibody Fab Light Chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2204
Polymers70,7963
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: C118 Antibody Fab Heavy Chain
M: C118 Antibody Fab Light Chain
S: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3664
Polymers70,7963
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.923, 89.993, 93.865
Angle α, β, γ (deg.)90.000, 113.334, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "H"
d_2ens_1(chain "I" and (resid 1 through 126 or resid 135 through 214))
d_1ens_2chain "L"
d_2ens_2(chain "M" and ((resid 1 and (name N or name...
d_1ens_3(chain "R" and (resid 321 through 502 or resid 600))
d_2ens_3(chain "S" and (resid 321 through 502 or resid 538))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSA1 - 220
d_21ens_1GLNPROB1 - 140
d_22ens_1THRLYSB142 - 221
d_11ens_2GLNTHRC1 - 214
d_21ens_2GLNTHRD1 - 214
d_11ens_3ASNGLUE1 - 182
d_21ens_3ASNGLUH1 - 182

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.99912321205, 0.039441154924, -0.0140428786682), (0.0386445963901, 0.997842422254, 0.0530763178854), (0.0161059713422, 0.0524870998311, -0.998491713555)71.454837768, -0.422184497905, -32.0201056644
2given(-0.99933278559, 0.0298245319911, 0.0210827165539), (0.0308546252566, 0.998254813553, 0.0503519544669), (-0.0195441998059, 0.050968858236, -0.998508988314)71.5397504514, 0.263484924633, -30.4190710453
3given(-0.997020849819, 0.0771263166684, 0.00097790806622), (0.0771016769865, 0.996900599928, -0.0156373037544), (-0.00218092477909, -0.0155153195263, -0.99987725168)70.5973578272, -0.567025533467, -30.8106529604

-
Components

#1: Antibody C118 Antibody Fab Heavy Chain


Mass: 25700.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody C118 Antibody Fab Light Chain


Mass: 22736.170 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: Protein Spike protein S1


Mass: 22359.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P59594
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium fluoride, 20% PEG 3,350

-
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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→46.61 Å / Num. obs: 72486 / % possible obs: 95.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 59.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0622 / Rpim(I) all: 0.0396 / Net I/σ(I): 13.14
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 3085 / CC1/2: 0.918 / Rpim(I) all: 0.28 / % possible all: 79.5

-
Processing

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

7k8m


Resolution: 2.7→46.61 Å / SU ML: 0.4387 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 3606 4.97 %
Rwork0.1946 68880 -
obs0.1972 72486 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.79 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9516 0 66 0 9582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00959839
X-RAY DIFFRACTIONf_angle_d1.16613413
X-RAY DIFFRACTIONf_chiral_restr0.06041486
X-RAY DIFFRACTIONf_plane_restr0.00971712
X-RAY DIFFRACTIONf_dihedral_angle_d13.16883484
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.08941338455
ens_2d_2MX-RAY DIFFRACTIONTorsion NCS1.52371244827
ens_3d_2SX-RAY DIFFRACTIONTorsion NCS0.811934711001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.48371010.40972007X-RAY DIFFRACTION70.79
2.74-2.770.37581120.37392269X-RAY DIFFRACTION81.15
2.77-2.810.42221310.34962387X-RAY DIFFRACTION85.53
2.81-2.860.40571420.31782596X-RAY DIFFRACTION94.19
2.86-2.90.41371470.28952771X-RAY DIFFRACTION98.02
2.9-2.950.33421520.27252715X-RAY DIFFRACTION97.98
2.95-30.2951410.26562747X-RAY DIFFRACTION97.44
3-3.050.3261310.24312693X-RAY DIFFRACTION97.41
3.05-3.110.29791550.25112768X-RAY DIFFRACTION97.05
3.11-3.180.32461410.23532661X-RAY DIFFRACTION97.02
3.18-3.240.28021440.23972738X-RAY DIFFRACTION96.42
3.24-3.320.27371390.23432639X-RAY DIFFRACTION94.33
3.32-3.40.31071380.2622697X-RAY DIFFRACTION96.13
3.4-3.50.2751440.2182698X-RAY DIFFRACTION97.6
3.5-3.60.27411480.22122751X-RAY DIFFRACTION97.87
3.6-3.710.36571320.20182742X-RAY DIFFRACTION97.49
3.71-3.850.24811390.20622667X-RAY DIFFRACTION97.03
3.85-40.24631340.18482727X-RAY DIFFRACTION96.36
4-4.180.20951350.18222619X-RAY DIFFRACTION93.9
4.18-4.40.21541360.15392757X-RAY DIFFRACTION97.64
4.4-4.680.1921440.13682738X-RAY DIFFRACTION97.63
4.68-5.040.17711470.13522688X-RAY DIFFRACTION97.19
5.04-5.550.19091300.15112687X-RAY DIFFRACTION95.3
5.55-6.350.1891480.15842720X-RAY DIFFRACTION97.85
6.35-7.990.19771550.17052710X-RAY DIFFRACTION96.69
7.99-46.610.19431400.14952688X-RAY DIFFRACTION96.06

+
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