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- PDB-6mef: Crystal structure of broadly neutralizing antibody AR3C -

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Basic information

Entry
Database: PDB / ID: 6mef
TitleCrystal structure of broadly neutralizing antibody AR3C
Components
  • antibody AR3C Heavy Chain
  • antibody AR3C Light Chain
KeywordsIMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFlyak, A.I. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127469 United States
CitationJournal: Cell Host Microbe / Year: 2018
Title: HCV Broadly Neutralizing Antibodies Use a CDRH3 Disulfide Motif to Recognize an E2 Glycoprotein Site that Can Be Targeted for Vaccine Design.
Authors: Flyak, A.I. / Ruiz, S. / Colbert, M.D. / Luong, T. / Crowe Jr., J.E. / Bailey, J.R. / Bjorkman, P.J.
History
DepositionSep 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: antibody AR3C Heavy Chain
L: antibody AR3C Light Chain


Theoretical massNumber of molelcules
Total (without water)48,8382
Polymers48,8382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-22 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.671, 146.870, 175.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody antibody AR3C Heavy Chain


Mass: 25571.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody antibody AR3C Light Chain


Mass: 23266.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.76 % / Mosaicity: 0.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2 M zinc acetate dihydrate pH 6.6, 11 % Sucrose, and 20% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→73.43 Å / Num. obs: 22315 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.076 / Rrim(I) all: 0.185 / Net I/σ(I): 8 / Num. measured all: 129027 / Scaling rejects: 158
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.086.11.57935630.5860.6951.729100
8.7-73.435.30.0689110.9850.0330.07699.5

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF

4mwf


Resolution: 2.9→56.283 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.25
RfactorNum. reflection% reflection
Rfree0.2561 1112 4.99 %
Rwork0.2214 --
obs0.2231 22266 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 267.95 Å2 / Biso mean: 78.1484 Å2 / Biso min: 25.33 Å2
Refinement stepCycle: final / Resolution: 2.9→56.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 0 3290
Num. residues----436
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)
10.00170.00820.00710.01950.00010.01050.0123-0.0054-0.03010.0827-0.08440.0146-0.05740.1524-0.00010.4877-0.1017-0.03010.3952-0.0050.3812-7.872-16.506-14.728
2-0.0005-0.0031-0.00130.00690.00550.0092-0.02270.0898-0.03180.0080.0182-0.02120.03670.084400.36630.0437-0.03550.6338-0.23540.5125-20.483-29.28-41.692
30.0515-0.0118-0.01010.0136-0.0120.0152-0.0018-0.06040.04670.042-0.0760.0631-0.1040.0117-0.02650.6423-0.0432-0.18340.2817-0.2330.3293-22.252-1.224-20.272
40.05020.00030.03890.01610.01940.0543-0.13190.0669-0.0288-0.0326-0.10620.0961-0.0163-0.1169-0.35660.0621-0.0125-0.11420.3381-0.4460.2984-36.645-26.952-41.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 127
2X-RAY DIFFRACTION2H128 - 215
3X-RAY DIFFRACTION3L1 - 107
4X-RAY DIFFRACTION4L108 - 212

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