[English] 日本語
Yorodumi
- PDB-7lk9: Crystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lk9
TitleCrystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23 HC + COVD21-C8 LC
Components
  • COV107-23 heavy chain
  • COVD21-C8 light chain
KeywordsIMMUNE SYSTEM / coronavirus / COVID-19 / SARS-CoV-2 / antibody / Fab / receptor binding domain
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYuan, M. / Zhu, X. / Wilson, I.A. / Wu, N.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI139445 United States
Citation
Journal: Nat Commun / Year: 2021
Title: Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain.
Authors: Tan, T.J.C. / Yuan, M. / Kuzelka, K. / Padron, G.C. / Beal, J.R. / Chen, X. / Wang, Y. / Rivera-Cardona, J. / Zhu, X. / Stadtmueller, B.M. / Brooke, C.B. / Wilson, I.A. / Wu, N.C.
#1: Journal: Biorxiv / Year: 2021
Title: Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain.
Authors: Tan, T.J.C. / Yuan, M. / Kuzelka, K. / Padron, G.C. / Beal, J.R. / Chen, X. / Wang, Y. / Rivera-Cardona, J. / Zhu, X. / Stadtmueller, B.M. / Brooke, C.B. / Wilson, I.A. / Wu, N.C.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
H: COV107-23 heavy chain
L: COVD21-C8 light chain
A: COV107-23 heavy chain
B: COVD21-C8 light chain
C: COV107-23 heavy chain
D: COVD21-C8 light chain
M: COV107-23 heavy chain
N: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)186,7768
Polymers186,7768
Non-polymers00
Water0
1
H: COV107-23 heavy chain
L: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area19400 Å2
MethodPISA
2
A: COV107-23 heavy chain
B: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-19 kcal/mol
Surface area19400 Å2
MethodPISA
3
C: COV107-23 heavy chain
D: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-21 kcal/mol
Surface area19380 Å2
MethodPISA
4
M: COV107-23 heavy chain
N: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-21 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.297, 78.383, 91.626
Angle α, β, γ (deg.)100.120, 112.090, 92.800
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain H
41chain M
12(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))
22(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))
32(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))
42chain N

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
111GLUGLUSERSERchain AAC1 - 2151 - 219
211GLUGLUSERSERchain CCE1 - 2151 - 219
311GLUGLUSERSERchain HHA1 - 2151 - 219
411GLUGLUSERSERchain MMG1 - 2151 - 219
112GLUGLUSERSER(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))BD1 - 71 - 7
122THRTHRPROPRO(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))BD10 - 1510 - 15
132ALAALAGLUGLU(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))BD19 - 21319 - 214
212GLUGLUSERSER(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))DF1 - 71 - 7
222THRTHRPROPRO(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))DF10 - 1510 - 15
232ALAALAGLUGLU(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))DF19 - 21319 - 214
312GLUGLUSERSER(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))LB1 - 71 - 7
322THRTHRPROPRO(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))LB10 - 1510 - 15
332ALAALAGLUGLU(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))LB19 - 21319 - 214
412GLUGLUGLUGLUchain NNH1 - 2131 - 214

NCS ensembles :
ID
1
2

-
Components

#1: Antibody
COV107-23 heavy chain


Mass: 23188.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
COVD21-C8 light chain


Mass: 23505.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M of sodium citrate pH 4, 1 M lithium chloride, and 20% (w/v) polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 24563 / % possible obs: 88 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.188 / Rrim(I) all: 0.354 / Χ2: 0.649 / Net I/σ(I): 2.1 / Num. measured all: 79514
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.42.60.70919700.7270.4640.8510.4983.4
3.4-3.512.80.60519960.7820.3980.7280.65286.6
3.51-3.632.90.58120790.7890.3780.6960.57789.5
3.63-3.7830.52520380.8170.3370.6260.62488.4
3.78-3.953.10.52620970.820.3390.6280.63689.4
3.95-4.163.20.40320770.890.2540.4780.59289.4
4.16-4.423.30.28919880.9410.1810.3420.61485.5
4.42-4.763.20.24718430.9550.1560.2930.72179.7
4.76-5.243.50.24820870.9590.1530.2920.62888.4
5.24-5.993.70.2721600.960.1620.3160.55895
5.99-7.553.70.25321850.9580.1510.2950.5293.7
7.55-503.70.08920430.9920.0540.1041.10287.5

-
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: 6XC2

6xc2


Resolution: 3.4→40.19 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3115 1087 4.85 %
Rwork0.2759 21308 -
obs0.2776 22395 88.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.17 Å2 / Biso mean: 62.1955 Å2 / Biso min: 35.17 Å2
Refinement stepCycle: final / Resolution: 3.4→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12881 0 0 0 12881
Num. residues----1707
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2568X-RAY DIFFRACTION6.831TORSIONAL
12C2568X-RAY DIFFRACTION6.831TORSIONAL
13H2568X-RAY DIFFRACTION6.831TORSIONAL
14M2568X-RAY DIFFRACTION6.831TORSIONAL
21B2507X-RAY DIFFRACTION6.831TORSIONAL
22D2507X-RAY DIFFRACTION6.831TORSIONAL
23L2507X-RAY DIFFRACTION6.831TORSIONAL
24N2507X-RAY DIFFRACTION6.831TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4001-3.55470.39871320.3569260587
3.5547-3.7420.37651320.3457269889
3.742-3.97630.35751380.325267689
3.9763-4.28290.3381300.2914267889
4.2829-4.71340.30191380.2581245782
4.7134-5.3940.28961400.2457265488
5.394-6.79050.30381480.2628284494
6.7905-40.190.22331290.2057269689

+
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