[English] 日本語
- PDB-7k8r: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibo... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 7k8r
TitleCrystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C135
  • C135 Fab Heavy Chain
  • C135 Fab Light Chain
KeywordsIMMUNE SYSTEM / Human Neutralizing Antibody / SARS-CoV-2 / Receptor Binding Domain / COVID-19
Biological speciesHomo sapiens (human)
AuthorsJette, C.A. / Barnes, C.O. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464-13 United States
Validation Report
SummaryFull reportAbout validation report
DepositionSep 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
H: C135 Fab Heavy Chain
L: C135 Fab Light Chain
hetero molecules

Theoretical massNumber of molelcules
Total (without water)47,4895

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-31 kcal/mol
Surface area19670 Å2
Unit cell
Length a, b, c (Å)102.258, 102.258, 53.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2


#1: Antibody C135 Fab Heavy Chain

Mass: 23686.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody C135 Fab Light Chain

Mass: 23526.041 Da / Num. of mol.: 1
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol

Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.04 M potassium phosphate, 16% w/v PEG8000, 20% v/v glycerol

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.28 Å / Num. obs: 72349 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 52.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 2.13 / Num. unique obs: 3071 / CC1/2: 0.305 / Rpim(I) all: 0.889


Blu-Icedata collection
XDSdata reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7BZ5
Resolution: 2→47.28 Å / SU ML: 0.3267 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 3860 5.34 %
Rwork0.195 68489 -
Obs0.1972 72349 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.85 Å2
Refinement stepCycle: LAST / Resolution: 2→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 0 30 3352
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01283411
X-RAY DIFFRACTIONf_angle_d1.17364638
X-RAY DIFFRACTIONf_chiral_restr0.0616518
X-RAY DIFFRACTIONf_plane_restr0.0073592
X-RAY DIFFRACTIONf_dihedral_angle_d19.97031216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2-2.020.36241230.38112260X-RAY DIFFRACTION90.95
2.02-2.050.33871420.35952450X-RAY DIFFRACTION98.74
2.05-2.080.33681340.3472391X-RAY DIFFRACTION99.14
2.08-2.110.34431350.33132461X-RAY DIFFRACTION99.5
2.11-2.140.32991400.32112466X-RAY DIFFRACTION97.02
2.14-2.170.33751360.3132388X-RAY DIFFRACTION99.53
2.17-2.20.34441420.31762458X-RAY DIFFRACTION100
2.2-2.240.36161420.31162450X-RAY DIFFRACTION99.42
2.24-2.280.32591360.30312474X-RAY DIFFRACTION99.92
2.28-2.320.31011440.27392465X-RAY DIFFRACTION99.81
2.32-2.360.30511340.26892443X-RAY DIFFRACTION99.65
2.36-2.410.30961460.26172502X-RAY DIFFRACTION100
2.41-2.460.24761380.24782440X-RAY DIFFRACTION99.81
2.46-2.520.32121360.24522462X-RAY DIFFRACTION100
2.52-2.580.27441390.23632472X-RAY DIFFRACTION99.89
2.58-2.650.271380.23892449X-RAY DIFFRACTION99.92
2.65-2.730.33941400.23982484X-RAY DIFFRACTION99.92
2.73-2.820.27271420.23432472X-RAY DIFFRACTION100
2.82-2.920.24531420.22162438X-RAY DIFFRACTION100
2.92-3.040.27311390.23082447X-RAY DIFFRACTION99.19
3.04-3.170.33461420.24152399X-RAY DIFFRACTION97.51
3.18-3.340.26111480.21882458X-RAY DIFFRACTION99.89
3.34-3.550.31861270.20382486X-RAY DIFFRACTION100
3.55-3.830.23161300.19092473X-RAY DIFFRACTION99.96
3.83-4.210.17051370.15822462X-RAY DIFFRACTION100
4.21-4.820.16651500.12622461X-RAY DIFFRACTION99.92
4.82-6.070.16141290.13442416X-RAY DIFFRACTION97.7
6.07-47.280.20061290.15432462X-RAY DIFFRACTION99.65

About Yorodumi


Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more


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.

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