[English] 日本語
Yorodumi
- PDB-7m3i: Structure of SARS-CoV-2 spike protein receptor binding domain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m3i
TitleStructure of SARS-CoV-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab
Components
  • CV2-75 Fab Heavy chain
  • CV2-75 Fab Light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / COVID-19 / Antibody / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHurlburt, N.K. / Pancera, M.
CitationJournal: Cell Rep / Year: 2021
Title: Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects.
Authors: Jennewein, M.F. / MacCamy, A.J. / Akins, N.R. / Feng, J. / Homad, L.J. / Hurlburt, N.K. / Seydoux, E. / Wan, Y.H. / Stuart, A.B. / Edara, V.V. / Floyd, K. / Vanderheiden, A. / Mascola, J.R. ...Authors: Jennewein, M.F. / MacCamy, A.J. / Akins, N.R. / Feng, J. / Homad, L.J. / Hurlburt, N.K. / Seydoux, E. / Wan, Y.H. / Stuart, A.B. / Edara, V.V. / Floyd, K. / Vanderheiden, A. / Mascola, J.R. / Doria-Rose, N. / Wang, L. / Yang, E.S. / Chu, H.Y. / Torres, J.L. / Ozorowski, G. / Ward, A.B. / Whaley, R.E. / Cohen, K.W. / Pancera, M. / McElrath, M.J. / Englund, J.A. / Finzi, A. / Suthar, M.S. / McGuire, A.T. / Stamatatos, L.
History
DepositionMar 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CV2-75 Fab Heavy chain
B: CV2-75 Fab Light chain
C: Spike protein S1
H: CV2-75 Fab Heavy chain
L: CV2-75 Fab Light chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,6778
Polymers155,2356
Non-polymers4422
Water28816
1
A: CV2-75 Fab Heavy chain
B: CV2-75 Fab Light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8394
Polymers77,6173
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-24 kcal/mol
Surface area30160 Å2
MethodPISA
2
H: CV2-75 Fab Heavy chain
L: CV2-75 Fab Light chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8394
Polymers77,6173
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-23 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.371, 127.519, 155.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 131 or resid 148 through 221))
21chain H
12chain B
22chain L
13chain C
23(chain R and (resid 321 through 532 or (resid 533...

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
111PCAPCAPROPRO(chain A and (resid 1 through 131 or resid 148 through 221))AA1 - 1311 - 131
121CYSCYSPROPRO(chain A and (resid 1 through 131 or resid 148 through 221))AA148 - 221148 - 221
211PCAPCAPROPROchain HHD1 - 2211 - 221
112SERSERTHRTHRchain BBB1 - 2111 - 211
212SERSERTHRTHRchain LLE1 - 2111 - 211
113GLNGLNNAGNAGchain CCC - G321 - 6003
213GLNGLNASNASN(chain R and (resid 321 through 532 or (resid 533...RF321 - 5323 - 214
223LEULEULEULEU(chain R and (resid 321 through 532 or (resid 533...RF533215
233GLNGLNNAGNAG(chain R and (resid 321 through 532 or (resid 533...RF - H321 - 6003
243GLNGLNNAGNAG(chain R and (resid 321 through 532 or (resid 533...RF - H321 - 6003
253GLNGLNNAGNAG(chain R and (resid 321 through 532 or (resid 533...RF - H321 - 6003
263GLNGLNNAGNAG(chain R and (resid 321 through 532 or (resid 533...RF - H321 - 6003

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody CV2-75 Fab Heavy chain


Mass: 24183.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#2: Antibody CV2-75 Fab Light chain


Mass: 22839.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#3: Protein Spike protein S1 / SARS-CoV-2 spike protein receptor binding domain


Mass: 30594.381 Da / Num. of mol.: 2 / 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): HEK293SGlycoDelete / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, pH 7.5, 0.1M Calcium acetate, 15% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→49.32 Å / Num. obs: 42799 / % possible obs: 99.48 % / Redundancy: 2 % / Biso Wilson estimate: 79.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 4141 / CC1/2: 0.566

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQQ, 6XE1

4fqq

6xe1


Resolution: 2.8→49.32 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 2092 4.89 %
Rwork0.2454 40707 -
obs0.2471 42799 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.18 Å2 / Biso mean: 101.1238 Å2 / Biso min: 33.95 Å2
Refinement stepCycle: final / Resolution: 2.8→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9830 0 28 16 9874
Biso mean--101.34 59.9 -
Num. residues----1282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310124
X-RAY DIFFRACTIONf_angle_d0.64413830
X-RAY DIFFRACTIONf_dihedral_angle_d11.6123598
X-RAY DIFFRACTIONf_chiral_restr0.0461544
X-RAY DIFFRACTIONf_plane_restr0.0051776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1783X-RAY DIFFRACTION15.748TORSIONAL
12H1783X-RAY DIFFRACTION15.748TORSIONAL
21B1838X-RAY DIFFRACTION15.748TORSIONAL
22L1838X-RAY DIFFRACTION15.748TORSIONAL
31C2022X-RAY DIFFRACTION15.748TORSIONAL
32R2022X-RAY DIFFRACTION15.748TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.40771330.36672581271497
2.87-2.940.39321430.344326782821100
2.94-3.020.38471330.321327012834100
3.02-3.110.31511500.301126762826100
3.11-3.210.35291440.296826872831100
3.21-3.320.33271400.267926962836100
3.32-3.450.32551390.259926782817100
3.45-3.610.2631430.248326892832100
3.61-3.80.31261100.254927192829100
3.8-4.040.2631380.236827402878100
4.04-4.350.25391330.210327212854100
4.35-4.790.22161470.19427262873100
4.79-5.480.25141630.211527282891100
5.48-6.90.29211320.25152779291199
6.9-49.320.26941440.25412908305299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.20462.26542.59984.53982.62784.5179-0.0210.09840.22570.0936-0.0029-0.07960.2247-0.09560.06730.4591-0.0518-0.04710.4390.20710.66651.3717.308-4.458
21.2227-0.13880.0745.70820.67953.60260.59690.2094-1.27970.147-0.1782-0.36320.62980.3279-0.30270.57540.0231-0.24440.39750.03681.164216.113-8.8-4.239
32.7236-2.253-0.52815.20651.1231.1731-0.2602-0.6363-0.43960.56640.2870.03590.10290.0184-0.02370.397-0.0281-0.00830.6010.16270.478627.03918.699.918
47.49063.8875-1.64995.2305-0.74082.97150.2182-0.4768-0.5096-0.2453-0.009-0.7307-0.33010.2871-0.18720.6337-0.09030.06830.7473-0.17260.480973.94940.38225.079
52.1528-1.6538-0.02264.0241.5435.35320.7627-1.13680.73060.6822-0.31970.2537-0.36430.1771-0.37160.9193-0.23640.21911.2916-0.26770.617357.64848.04937.44
63.724-0.3085-1.14292.47850.71572.84-0.1155-0.4872-0.37230.23350.15650.00750.089-0.1891-0.0410.5297-0.0271-0.0970.70590.05560.432247.95624.79116.663
78.08931.641-0.86767.2469-1.79235.53840.1347-0.04050.20241.0505-0.59140.51570.7162-0.51580.32530.9031-0.24640.14340.774-0.16240.5807-19.77-15.65-11.546
89.1305-2.05882.98477.7257-1.14342.257-0.0993-0.07940.60120.2689-0.1874-0.42760.2688-0.36730.28150.7057-0.24740.10050.9989-0.1280.4365-13.493-24.51-23.669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:122 )A1 - 122
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:108 )B1 - 108
3X-RAY DIFFRACTION3( CHAIN C AND RESID 321:537 )C321 - 537
4X-RAY DIFFRACTION4( CHAIN H AND RESID 1:122 )H1 - 122
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:108 )L1 - 108
6X-RAY DIFFRACTION6( CHAIN R AND RESID 321:537 )R321 - 537
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:221 )A123 - 221
8X-RAY DIFFRACTION8( CHAIN B AND RESID 109:211 )B109 - 211

+
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