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- PDB-6med: Crystal structure of broadly neutralizing antibody HEPC3 -

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Basic information

Entry
Database: PDB / ID: 6med
TitleCrystal structure of broadly neutralizing antibody HEPC3
Components
  • antibody HEPC3 Heavy Chain
  • antibody HEPC3 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: 2.04 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 2.0Nov 6, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.pdbx_PDB_ins_code ..._atom_site.auth_seq_id / _atom_site.pdbx_PDB_ins_code / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_PDB_ins_code / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.PDB_ins_code_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct.title / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.pdbx_beg_PDB_ins_code / _struct_sheet_range.pdbx_end_PDB_ins_code / _struct_site_gen.auth_seq_id / _struct_site_gen.pdbx_auth_ins_code
Revision 2.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody HEPC3 Heavy Chain
B: antibody HEPC3 Light Chain
C: antibody HEPC3 Heavy Chain
D: antibody HEPC3 Light Chain
G: antibody HEPC3 Heavy Chain
I: antibody HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,98612
Polymers146,4106
Non-polymers5766
Water18,0151000
1
A: antibody HEPC3 Heavy Chain
B: antibody HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0915
Polymers48,8032
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-45 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: antibody HEPC3 Heavy Chain
D: antibody HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8993
Polymers48,8032
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-47 kcal/mol
Surface area19430 Å2
MethodPISA
3
G: antibody HEPC3 Heavy Chain
I: antibody HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9954
Polymers48,8032
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-45 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.910, 108.690, 166.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody antibody HEPC3 Heavy Chain


Mass: 25418.410 Da / Num. of mol.: 3
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 HEPC3 Light Chain


Mass: 23384.883 Da / Num. of mol.: 3
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1000 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.91 % / Mosaicity: 0.33 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 2.0M ammonium sulfate, 0.3M sodium chloride, and 0.1M sodium cacodylate pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.04→85 Å / Num. obs: 114454 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 32.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.054 / Rrim(I) all: 0.115 / Net I/σ(I): 9.2 / Num. measured all: 502647 / Scaling rejects: 224
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
2.04-2.074.31.052427556000.540.5591.1941.499.9
11.17-8540.0329947550.9990.0160.03421.395.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF

4mwf


Resolution: 2.04→39.583 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 5624 4.92 %
Rwork0.1815 108723 -
obs0.1832 114347 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.48 Å2 / Biso mean: 40.6303 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 2.04→39.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9889 0 30 1002 10921
Biso mean--44.93 41.92 -
Num. residues----1305
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 (%)
2.04-2.06320.32571830.28435563739100
2.0632-2.08750.32361710.273835903761100
2.0875-2.11290.28241990.256335893788100
2.1129-2.13970.29021940.254935653759100
2.1397-2.16780.30851770.239235813758100
2.1678-2.19750.25721840.238636013785100
2.1975-2.22890.28331870.226535983785100
2.2289-2.26220.28481870.23136003787100
2.2622-2.29750.27281770.218135983775100
2.2975-2.33520.29591870.210935793766100
2.3352-2.37540.23511770.201936153792100
2.3754-2.41860.26191940.20636053799100
2.4186-2.46510.25862080.196835753783100
2.4651-2.51540.26371900.195335763766100
2.5154-2.57010.23781840.185635973781100
2.5701-2.62990.2331910.181336043795100
2.6299-2.69570.2221890.183636093798100
2.6957-2.76850.23631780.189936483826100
2.7685-2.850.23821790.192536103789100
2.85-2.94190.24111930.195536163809100
2.9419-3.0470.22281620.180736303792100
3.047-3.1690.21031830.178336343817100
3.169-3.31320.23371710.178236723843100
3.3132-3.48770.20251870.172836353822100
3.4877-3.70610.20342200.156336143834100
3.7061-3.9920.19672020.151236523854100
3.992-4.39330.16171990.131936613860100
4.3933-5.02790.15182010.131336953896100
5.0279-6.33040.17661950.17137363931100
6.3304-39.59050.20911750.21663882405799

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