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- PDB-6meg: Crystal structure of human monoclonal antibody HEPC46 -

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Basic information

Entry
Database: PDB / ID: 6meg
TitleCrystal structure of human monoclonal antibody HEPC46
Components
  • antibody HEPC46 Heavy Chain
  • antibody HEPC46 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: 1.41 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: antibody HEPC46 Heavy Chain
L: antibody HEPC46 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,6202
Polymers47,6202
Non-polymers00
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-22 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.640, 71.302, 108.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody antibody HEPC46 Heavy Chain


Mass: 24681.619 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 HEPC46 Light Chain


Mass: 22938.188 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.36 % / Mosaicity: 0.44 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 30% PEG 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→48.81 Å / Num. obs: 81686 / % possible obs: 99.2 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Rrim(I) all: 0.071 / Net I/σ(I): 11.1 / Num. measured all: 402521 / Scaling rejects: 227
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
1.41-1.4350.8932004840030.640.4290.9951.699.8
7.72-48.815.40.0431225750.9970.0180.04430.998.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P30

3p30


Resolution: 1.41→33.872 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 4072 4.99 %
Rwork0.1743 77538 -
obs0.1756 81610 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.17 Å2 / Biso mean: 27.164 Å2 / Biso min: 9.54 Å2
Refinement stepCycle: final / Resolution: 1.41→33.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 597 3821
Biso mean---33.19 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093309
X-RAY DIFFRACTIONf_angle_d1.0414521
X-RAY DIFFRACTIONf_chiral_restr0.088509
X-RAY DIFFRACTIONf_plane_restr0.008578
X-RAY DIFFRACTIONf_dihedral_angle_d13.5021177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.41-1.42660.28991490.285326592808100
1.4266-1.4440.31821270.281226512778100
1.444-1.46230.3271420.277826602802100
1.4623-1.48150.27171260.27127022828100
1.4815-1.50180.25961260.247926332759100
1.5018-1.52330.30771400.243326802820100
1.5233-1.5460.23451520.23982621277399
1.546-1.57020.23671340.22792579271397
1.5702-1.59590.25531360.22012591272797
1.5959-1.62340.24821380.216126882826100
1.6234-1.65290.2631480.213626672815100
1.6529-1.68470.24611500.210426282778100
1.6847-1.71910.22981380.199627032841100
1.7191-1.75650.2341360.200126812817100
1.7565-1.79730.23791350.198626562791100
1.7973-1.84230.24581370.19392671280899
1.8423-1.89210.21521350.1862595273096
1.8921-1.94780.19811460.17926842830100
1.9478-2.01060.21071590.176726662825100
2.0106-2.08250.20891400.169126812821100
2.0825-2.16580.19221490.17326952844100
2.1658-2.26440.19741350.1652691282699
2.2644-2.38380.19991530.16432638279198
2.3838-2.53310.17161350.1652659279498
2.5331-2.72860.16481360.16342719285599
2.7286-3.0030.20581330.1612713284699
3.003-3.43720.19141370.16012723286098
3.4372-4.32910.14751480.14527632911100
4.3291-33.8820.18291520.14942841299397
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)
10.48210.0622-0.24250.2311-0.07770.55020.2783-0.02560.4029-0.05750.0701-0.02-0.3099-0.1784-0.03570.26660.08640.20510.13250.01160.299327.19537.114113.611
21.6826-0.0432-0.14721.4735-0.17121.2176-0.08390.0759-0.1725-0.0442-0.0368-0.0049-0.07820.16530.11490.1294-0.00160.00210.14440.01770.111423.43225.18683.954
31.0269-0.25560.06161.01790.17161.82280.1055-0.0616-0.1168-0.0460.06620.01910.0157-0.0005-0.15110.0848-0.001-0.01560.1090.00870.116126.3216.121119.076
40.8031-0.07220.20171.5718-0.46431.22150.10010.02740.0102-0.1849-0.1056-0.13480.1385-0.01330.00960.15830.00850.00760.14030.01670.122333.98813.30781.715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:118 )H1 - 118
2X-RAY DIFFRACTION2( CHAIN H AND RESID 119:214 )H119 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:111 )L1 - 111
4X-RAY DIFFRACTION4( CHAIN L AND RESID 112:209 )L112 - 209

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