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- PDB-6meh: Crystal structure of broadly neutralizing antibody HEPC74 in comp... -

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Basic information

Entry
Database: PDB / ID: 6meh
TitleCrystal structure of broadly neutralizing antibody HEPC74 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • (antibody HEPC74 ...) x 2
  • E2 glycoprotein
KeywordsIMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies
Function / homology
Function and homology information


host cell lipid droplet / host cell mitochondrion / viral nucleocapsid / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell ...host cell lipid droplet / host cell mitochondrion / viral nucleocapsid / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity
Similarity search - Function
Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepacivirus C
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 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
C: E2 glycoprotein
H: antibody HEPC74 Heavy Chain
L: antibody HEPC74 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3148
Polymers77,8023
Non-polymers1,5125
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-14 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.309, 69.770, 168.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody antibody HEPC74 Heavy Chain


Mass: 25385.461 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: Antibody antibody HEPC74 Light Chain


Mass: 23470.111 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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Protein / Non-polymers , 2 types, 404 molecules C

#1: Protein E2 glycoprotein


Mass: 28946.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Plasmid: pCMV / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE26
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 2.51 Å3/Da / Density % sol: 50.92 % / Mosaicity: 0.36 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1% tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH 7.0, 20% 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: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→84.29 Å / Num. obs: 53916 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 36.04 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Net I/σ(I): 7.3 / Num. measured all: 317427 / Scaling rejects: 465
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.99-2.044.91.13832610.0260.6641.33787
9.11-84.295.60.0536750.9950.0240.05999.4

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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, 6MEE

4mwf

6mee


Resolution: 1.99→43.764 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2298 2692 5.01 %
Rwork0.1862 --
obs0.1883 53774 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.32 Å2 / Biso mean: 50.8678 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 1.99→43.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 98 403 5089
Biso mean--83.42 48.69 -
Num. residues----603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9887-2.02480.35881260.30042176230282
2.0248-2.06380.31781320.26962691282399
2.0638-2.10590.2741320.23692662279499
2.1059-2.15170.22551320.22927022834100
2.1517-2.20170.27921630.230426612824100
2.2017-2.25680.35341360.270527012837100
2.2568-2.31780.35311360.29752623275998
2.3178-2.3860.24861630.22462679284299
2.386-2.4630.25971540.21182674282899
2.463-2.5510.25091310.20062682281399
2.551-2.65320.24631630.197126882851100
2.6532-2.77390.27761530.196627132866100
2.7739-2.92010.28951140.200227392853100
2.9201-3.1030.25711140.203927472861100
3.103-3.34250.22361380.19692736287499
3.3425-3.67880.23031310.17727732904100
3.6788-4.21070.20751780.159627202898100
4.2107-5.30360.16321600.125727832943100
5.3036-43.77420.19381360.16782932306899
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)
11.3047-0.0987-0.1671.20830.48955.3430.0420.36420.1783-0.0844-0.0204-0.0213-0.5118-0.6906-0.01780.33410.110.02570.43920.05180.318613.444-8.121-36.968
23.5024-2.0741.11172.4316-0.45772.0029-0.04680.02620.11120.1171-0.0575-0.0653-0.11080.03550.10020.2516-0.01430.00560.17460.00590.2627.625-19.158-7.44
30.98110.2907-0.61631.56280.38083.4313-0.08550.5344-0.16830.0313-0.00010.15970.6009-1.04610.01860.38-0.2454-0.00090.7465-0.07520.33486.885-28.726-36.299
42.4193-0.1927-0.6642.7271.44025.1604-0.0542-0.1278-0.24070.0540.0440.06220.1868-0.028-0.00730.2125-0.0074-0.01980.12230.01970.302815.23-27.373-0.787
53.33421.32761.84811.68681.80333.7438-0.33670.11360.1957-0.0409-0.01680.1645-0.1306-0.00250.34940.4291-0.0230.04910.5650.01660.387113.83-13.421-58.516
68.22243.03434.62053.03342.73947.88880.0720.1466-2.0343-0.56320.6788-1.55711.12831.0116-0.32450.9328-0.04510.29130.6067-0.06061.059726.186-21.009-71.124
71.30290.07271.31341.74390.77671.6602-0.93650.5923-0.8154-0.63230.3486-0.27531.0573-1.3710.44250.72-0.35470.18520.7187-0.16970.50757.438-21.625-72.046
84.5387-0.2943-2.24713.3370.8955.966-0.82980.8555-0.8712-1.30020.1674-0.28270.8063-0.35230.56090.7723-0.26480.21740.5158-0.11440.581217.744-19.697-75.918
98.4676-3.68831.21877.32213.48219.4474-0.61191.0434-1.242-0.82550.6271-1.72891.21021.5857-0.17380.7969-0.16470.21790.7051-0.15860.760828.95-14.168-77.911
103.57590.6294-2.18063.046-2.44824.11330.08780.0811-0.0549-0.0469-0.11350.0819-0.25580.02840.0550.4473-0.14850.04250.3424-0.03440.336922.675-5.865-75.454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:125 )H1 - 125
2X-RAY DIFFRACTION2( CHAIN H AND RESID 126:215 )H126 - 215
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:108 )L1 - 108
4X-RAY DIFFRACTION4( CHAIN L AND RESID 109:213 )L109 - 213
5X-RAY DIFFRACTION5( CHAIN C AND RESID 418:451 )C418 - 451
6X-RAY DIFFRACTION6( CHAIN C AND RESID 452:495 )C452 - 495
7X-RAY DIFFRACTION7( CHAIN C AND RESID 496:538 )C496 - 538
8X-RAY DIFFRACTION8( CHAIN C AND RESID 539:566 )C539 - 566
9X-RAY DIFFRACTION9( CHAIN C AND RESID 567:606 )C567 - 606
10X-RAY DIFFRACTION10( CHAIN C AND RESID 607:645 )C607 - 645

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