[English] 日本語
Yorodumi
- PDB-7n3h: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n3h
TitleCrystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment C099
Components
  • C099 Fab Heavy Chain
  • C099 Fab Light Chain
KeywordsIMMUNE SYSTEM / severe acute respiratory syndrome coronavirus-2 / spike protein / neutralizing antibodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsFlyak, A.I. / Bjorkman, P.J. / Barnes, C.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI153465 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
Citation
Journal: Immunity / Year: 2021
Title: Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations.
Authors: Frauke Muecksch / Yiska Weisblum / Christopher O Barnes / Fabian Schmidt / Dennis Schaefer-Babajew / Zijun Wang / Julio C C Lorenzi / Andrew I Flyak / Andrew T DeLaitsch / Kathryn E Huey- ...Authors: Frauke Muecksch / Yiska Weisblum / Christopher O Barnes / Fabian Schmidt / Dennis Schaefer-Babajew / Zijun Wang / Julio C C Lorenzi / Andrew I Flyak / Andrew T DeLaitsch / Kathryn E Huey-Tubman / Shurong Hou / Celia A Schiffer / Christian Gaebler / Justin Da Silva / Daniel Poston / Shlomo Finkin / Alice Cho / Melissa Cipolla / Thiago Y Oliveira / Katrina G Millard / Victor Ramos / Anna Gazumyan / Magdalena Rutkowska / Marina Caskey / Michel C Nussenzweig / Pamela J Bjorkman / Theodora Hatziioannou / Paul D Bieniasz /
Abstract: Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute ...Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) Spike receptor-binding domain (RBD)-specific antibodies from 5 individuals shortly after infection and later in convalescence to determine the impact of maturation over months. In addition to increased affinity and neutralization potency, antibody evolution changed the mutational pathways for the acquisition of viral resistance and restricted neutralization escape options. For some antibodies, maturation imposed a requirement for multiple substitutions to enable escape. For certain antibodies, affinity maturation enabled the neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.
#1: Journal: bioRxiv / Year: 2021
Title: Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies.
Authors: Frauke Muecksch / Yiska Weisblum / Christopher O Barnes / Fabian Schmidt / Dennis Schaefer-Babajew / Julio C C Lorenzi / Andrew I Flyak / Andrew T DeLaitsch / Kathryn E Huey-Tubman / Shurong ...Authors: Frauke Muecksch / Yiska Weisblum / Christopher O Barnes / Fabian Schmidt / Dennis Schaefer-Babajew / Julio C C Lorenzi / Andrew I Flyak / Andrew T DeLaitsch / Kathryn E Huey-Tubman / Shurong Hou / Celia A Schiffer / Christian Gaebler / Zijun Wang / Justin Da Silva / Daniel Poston / Shlomo Finkin / Alice Cho / Melissa Cipolla / Thiago Y Oliveira / Katrina G Millard / Victor Ramos / Anna Gazumyan / Magdalena Rutkowska / Marina Caskey / Michel C Nussenzweig / Pamela J Bjorkman / Theodora Hatziioannou / Paul D Bieniasz /
Abstract: Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on ...Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.
History
DepositionJun 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: C099 Fab Heavy Chain
L: C099 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,7022
Polymers47,7022
Non-polymers00
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-26 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.100, 92.580, 115.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody C099 Fab Heavy Chain


Mass: 24403.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#2: Antibody C099 Fab Light Chain


Mass: 23298.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 % / Mosaicity: 0.5 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.9 M ammonium sulfate, citric acid pH 3.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.26→57.58 Å / Num. obs: 116022 / % possible obs: 90.9 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.043 / Rrim(I) all: 0.105 / Net I/σ(I): 8.3 / Num. measured all: 653930 / Scaling rejects: 922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.26-1.285.51.8883392161480.4440.8722.0870.998.6
6.9-57.586.30.0557919150.9930.0210.05424.199.7

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC4

6xc4


Resolution: 1.26→42.95 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 5823 5.03 %
Rwork0.1802 109842 -
obs0.1812 115665 90.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.76 Å2 / Biso mean: 21.0463 Å2 / Biso min: 7.16 Å2
Refinement stepCycle: final / Resolution: 1.26→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 0 632 3834
Biso mean---30.42 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093354
X-RAY DIFFRACTIONf_angle_d1.074587
X-RAY DIFFRACTIONf_dihedral_angle_d19.9591232
X-RAY DIFFRACTIONf_chiral_restr0.082524
X-RAY DIFFRACTIONf_plane_restr0.007590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.26-1.270.27952100.30833851406198
1.27-1.290.38241930.34693910410397
1.29-1.310.36652010.36023962416398
1.31-1.320.29012180.29173854407297
1.32-1.340.2862100.27163847405796
1.34-1.360.2911850.26533721390693
1.36-1.380.27672220.25713929415198
1.38-1.40.28641900.23713953414399
1.4-1.420.2462420.22923959420199
1.42-1.440.24131950.233949414499
1.44-1.470.22861300.23152601273164
1.47-1.490.25441240.2132573269764
1.49-1.520.21782050.1963950415597
1.52-1.550.22981360.18982680281667
1.55-1.590.18872230.18493735395893
1.59-1.620.19222020.1784028423099
1.62-1.670.18332290.168839654194100
1.67-1.710.19632090.16654010421999
1.71-1.760.19372270.1583975420299
1.76-1.820.17072060.15393956416298
1.82-1.880.16252110.15993968417998
1.88-1.950.2658790.21781584166344
1.96-2.050.18362060.14993592379897
2.05-2.150.16331690.14913376354583
2.15-2.290.24142020.19153238344080
2.29-2.470.19362010.16494068426999
2.47-2.710.1872050.16323676388190
2.71-3.110.18622010.16494035423697
3.11-3.890.1981660.15423771393791
3.93-42.950.16232260.16874126435296
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)
10.99930.1805-0.36612.22590.61880.963-0.0588-0.0625-0.14160.00980.0264-0.01240.05930.04170.02480.07830.00470.00570.0914-0.02410.097-2.12139.38830.232
22.39120.3135-0.55410.66550.13680.9538-0.0054-0.0669-0.04610.03190.034-0.07310.01340.1352-0.02610.09480.0095-0.01090.08750.01750.075615.815.36618.696
31.9214-0.3562-0.56611.71980.23721.55240.02890.02160.1186-0.0908-0.0159-0.1159-0.07370.073-0.00490.0998-0.01450.01540.0946-0.02770.08678.05949.05512.538
40.71160.3617-0.25343.36110.31721.0433-0.0030.0461-0.0235-0.0288-0.00270.09180.1033-0.02350.01560.07310.0043-0.00190.105-0.0010.068615.79312.9642.511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:118 )H2 - 118
2X-RAY DIFFRACTION2( CHAIN H AND RESID 119:214 )H119 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:108 )L1 - 108
4X-RAY DIFFRACTION4( CHAIN L AND RESID 109:213 )L109 - 213

+
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