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- PDB-6mee: Crystal structure of broadly neutralizing antibody HEPC74 -

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Basic information

Entry
Database: PDB / ID: 6mee
TitleCrystal structure of broadly neutralizing antibody HEPC74
Components
  • antibody HEPC74 Heavy Chain
  • antibody HEPC74 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: 1.36 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 20, 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
A: antibody HEPC74 Heavy Chain
B: antibody HEPC74 Light Chain
C: antibody HEPC74 Heavy Chain
D: antibody HEPC74 Light Chain


Theoretical massNumber of molelcules
Total (without water)97,7114
Polymers97,7114
Non-polymers00
Water25,1851398
1
A: antibody HEPC74 Heavy Chain
B: antibody HEPC74 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,8562
Polymers48,8562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-24 kcal/mol
Surface area20110 Å2
MethodPISA
2
C: antibody HEPC74 Heavy Chain
D: antibody HEPC74 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,8562
Polymers48,8562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-22 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.130, 63.586, 73.760
Angle α, β, γ (deg.)80.310, 74.110, 83.730
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody antibody HEPC74 Heavy Chain


Mass: 25385.461 Da / Num. of mol.: 2
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 HEPC74 Light Chain


Mass: 23470.111 Da / Num. of mol.: 2
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.: 1398 / 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: 2.5 Å3/Da / Density % sol: 50.86 % / Mosaicity: 0.6 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1M BIS-Tris pH5.5, and 25% PEG 3,350

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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: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→39.13 Å / Num. obs: 190823 / % possible obs: 93.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 11.5 / Num. measured all: 1209314 / Scaling rejects: 340
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
1.36-1.386.31.375862293510.4510.5871.4951.392.1
7.45-39.137.80.042952612140.9990.0160.04438.898.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF

4mwf


Resolution: 1.36→35.097 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 9561 5.01 %
Rwork0.1673 181234 -
obs0.1684 190795 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.45 Å2 / Biso mean: 28.5449 Å2 / Biso min: 9.3 Å2
Refinement stepCycle: final / Resolution: 1.36→35.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 0 1404 7996
Biso mean---36.07 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096753
X-RAY DIFFRACTIONf_angle_d1.0639202
X-RAY DIFFRACTIONf_chiral_restr0.0881054
X-RAY DIFFRACTIONf_plane_restr0.0081167
X-RAY DIFFRACTIONf_dihedral_angle_d15.5532444
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 (%)
1.36-1.37550.32642940.32825964625892
1.3755-1.39160.31893350.31225948628392
1.3916-1.40860.33152970.30196001629893
1.4086-1.42640.32763290.29285896622592
1.4264-1.44520.34532870.29395959624691
1.4452-1.4650.31723350.27685836617192
1.465-1.48590.29673300.25936013634393
1.4859-1.50810.26743150.24015955627092
1.5081-1.53170.28793110.24236102641393
1.5317-1.55680.22893240.21925966629094
1.5568-1.58360.23583230.20716018634193
1.5836-1.61240.22863320.20345931626392
1.6124-1.64350.23173190.20286074639394
1.6435-1.6770.21323100.19546078638894
1.677-1.71350.21963300.19266030636094
1.7135-1.75330.2033030.19075973627693
1.7533-1.79720.23063100.18466028633893
1.7972-1.84580.21563180.18426157647595
1.8458-1.90010.23490.17526064641395
1.9001-1.96140.17633310.16736052638395
1.9614-2.03150.17163400.15936190653095
2.0315-2.11280.18742710.15966146641794
2.1128-2.20890.18073240.15716049637394
2.2089-2.32540.18233430.15736125646896
2.3254-2.4710.173260.15676211653796
2.471-2.66180.18312970.1526203650096
2.6618-2.92950.18673300.15256019634993
2.9295-3.35310.17073150.15246137645295
3.3531-4.22350.17443200.14476149646995
4.2235-35.10880.14513130.13395960627393
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)
10.7936-0.2360.33620.8162-0.12580.6690.0111-0.0998-0.05870.0661-0.06-0.10290.16110.0176-0.01150.13210.0042-0.01390.12920.02110.14734.417-74.30152.158
20.59670.02480.10730.3308-0.28840.7078-0.0141-0.2462-0.05280.0739-0.0094-0.0668-0.2503-0.08320.00010.1830.0536-0.0070.22550.00420.135549.235-42.47141.366
30.51210.0005-0.21830.9186-0.24210.38460.0114-0.014-0.0124-0.0913-0.02270.0210.0646-0.08680.00020.1126-0.0049-0.01920.1201-0.01250.11818.754-64.8940.852
40.51590.31490.07790.2557-0.10730.6736-0.0270.11550.0303-0.00220.0044-0.0074-0.04120.0281-00.12310.01620.00310.14240.01710.156244.347-45.55425.876
50.5225-0.2088-0.38471.03760.49050.53070.0493-0.0177-0.0092-0.0029-0.0281-0.0665-0.15050.17250.00950.1577-0.0354-0.00070.1645-0.01090.138752.539-50.945-10.712
60.53980.08620.44761.0080.09240.72950.03430.0837-0.0769-0.0191-0.09590.09270.1656-0.16870.00010.1978-0.02460.0090.1918-0.04540.131726.382-72.7631.943
70.56970.3187-0.26020.8241-0.22140.70730.0298-0.00140.10050.01370.0570.0834-0.21470.03660.00010.1891-0.01660.00910.12550.00170.14240.032-38.2461.229
80.4233-0.0631-0.34280.3802-0.0541.0607-0.05450.0238-0.01120.0354-0.0074-0.01260.0924-0.0324-0.00050.183-0.0060.0070.1165-0.01410.147227.835-67.30616.739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:125 )A2 - 125
2X-RAY DIFFRACTION2( CHAIN A AND RESID 126:215 )A126 - 215
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:110 )B1 - 110
4X-RAY DIFFRACTION4( CHAIN B AND RESID 111:213 )B111 - 213
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:125 )C1 - 125
6X-RAY DIFFRACTION6( CHAIN C AND RESID 126:215 )C126 - 215
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:110 )D1 - 110
8X-RAY DIFFRACTION8( CHAIN D AND RESID 111:213 )D111 - 213

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