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- PDB-6mej: Crystal structure of Hepatitis C virus envelope glycoprotein E2 e... -

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Basic information

Entry
Database: PDB / ID: 6mej
TitleCrystal structure of Hepatitis C virus envelope glycoprotein E2 ectodomain in complex with human antibodies HEPC3 and HEPC46
Components
  • (antibody HEPC3 ...) x 2
  • (antibody HEPC46 ...) x 2
  • E2 glycoprotein
KeywordsIMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies
Function / homology
Function and homology information


host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / apoptotic process / viral envelope / host cell nucleus / virion membrane ...host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / apoptotic process / viral envelope / host cell nucleus / virion membrane / structural molecule activity / cytoplasm
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 speciesHomo sapiens (human)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 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 HEPC46 Heavy Chain
B: antibody HEPC46 Light Chain
C: E2 glycoprotein
H: antibody HEPC3 Heavy Chain
L: antibody HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,07811
Polymers125,5345
Non-polymers2,5446
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-15 kcal/mol
Surface area49100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.440, 76.640, 118.260
Angle α, β, γ (deg.)90.000, 106.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules C

#3: Protein E2 glycoprotein


Mass: 28769.514 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: C1KH25

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Antibody , 4 types, 4 molecules ABHL

#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)
#4: Antibody antibody HEPC3 Heavy Chain


Mass: 25759.807 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)
#5: Antibody antibody HEPC3 Light Chain


Mass: 23384.883 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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Sugars , 3 types, 6 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a3-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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.: 4
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: 2.99 Å3/Da / Density % sol: 58.93 % / Mosaicity: 0.5 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.2 M Ammonium sulfate, 20% Peg 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→78.27 Å / Num. obs: 45937 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 64.62 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.085 / Rrim(I) all: 0.152 / Net I/σ(I): 5.6 / Num. measured all: 142433 / Scaling rejects: 109
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.691.6411399545020.2581.1442.0090.799.9
10.07-78.270.04926598540.9950.0330.05916.499.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF, 6MED, 6MEG

4mwf

6med

6meg


Resolution: 2.8→78.271 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 1806 4.92 %
Rwork0.1984 34930 -
obs0.2019 36736 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.09 Å2 / Biso mean: 75.0984 Å2 / Biso min: 24.8 Å2
Refinement stepCycle: final / Resolution: 2.8→78.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8333 0 167 0 8500
Biso mean--102.37 --
Num. residues----1099
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.87570.4691260.34142681280799
2.8757-2.96040.36451290.297126792808100
2.9604-3.05590.3671420.275826612803100
3.0559-3.16510.32871350.268626402775100
3.1651-3.29190.33161450.249826752820100
3.2919-3.44170.29511500.2162650280099
3.4417-3.62310.26271510.20822668281999
3.6231-3.85010.27971410.202926822823100
3.8501-4.14740.30731340.191726832817100
4.1474-4.56470.26341230.160627132836100
4.5647-5.22510.21531440.155127002844100
5.2251-6.58260.28761450.178727052850100
6.5826-78.30110.18781410.179227932934100
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)
12.2867-0.3147-0.60591.58490.62041.18310.1212-0.1417-0.14740.082-0.35570.1082-0.0021-0.2744-0.00020.3093-0.0516-0.00850.3891-0.0160.3299-40.29112.925-88.436
21.6364-0.036-0.16020.81130.00290.08620.1841-0.28980.2722-0.0479-0.0020.08230.3416-0.1474-0.00030.5696-0.072800.6176-0.0440.6299-65.5650.002-117.745
30.6650.08960.43490.80490.44571.90460.22570.6909-0.3365-0.2048-0.2650.0491-0.14140.1341-0.00380.39840.1907-0.0270.4128-0.17710.5112-27.0995.017-103.772
40.95610.48780.52162.03930.81331.0256-0.05580.05580.3306-0.10.1438-0.3707-0.0887-0.21740.00050.5672-0.04660.08880.48850.04090.7059-51.1147.942-120.477
50.77440.68620.48260.55750.31860.7388-0.0763-0.02040.3376-0.0793-0.00360.04050.0995-0.20900.47930.0164-0.01780.76490.13950.4799-9.6423.515-57.949
60.13790.3195-0.20730.6269-0.45640.30980.32710.6113-0.4122-0.19390.1445-0.36470.78370.5682-0.00030.9256-0.0063-0.0550.97150.05560.8722-1.63719.647-85.188
70.4472-0.31220.2250.2626-0.24520.25820.3114-0.2714-0.3438-0.1269-0.07970.12420.3212-0.2746-0.00050.4766-0.1244-0.01690.58130.15550.4723-17.3714.51-69.38
80.4330.2335-0.0881.51660.85620.54350.08370.0261-0.0803-0.2130.17190.392-0.1009-0.19690.00070.5058-0.0122-0.03980.51370.09610.4457-11.10127.041-81.648
92.7957-0.06850.87031.8553-0.25871.2239-0.153-0.16970.29150.0870.14-0.1413-0.241-0.4141-0.00010.53450.0611-0.05830.41460.01850.46787.91129.577-42.666
101.05050.48460.20261.4451.27741.5684-0.0360.06650.13310.1957-0.111-0.169-0.13690.1451-0.00030.387-0.0681-0.02330.27270.04220.334837.76517.047-29.491
111.70140.17811.15851.4004-0.01921.07950.1281-0.5829-0.52960.11480.163-0.08530.0092-0.72620.00250.4421-0.09040.01960.74410.20880.48472.20110.27-36.122
121.14040.44030.5622.4316-0.62621.6574-0.102-0.353-0.05290.17920.1647-0.2066-0.0786-0.0605-0.00030.43650.00320.07150.4943-0.02060.395932.84712.385-15.036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:118 )A1 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 119:214 )A119 - 214
3X-RAY DIFFRACTION3( CHAIN B AND RESID 2:110 )B2 - 110
4X-RAY DIFFRACTION4( CHAIN B AND RESID 111:209 )B111 - 209
5X-RAY DIFFRACTION5( CHAIN C AND RESID 405:451 )C405 - 451
6X-RAY DIFFRACTION6( CHAIN C AND RESID 452:490 )C452 - 490
7X-RAY DIFFRACTION7( CHAIN C AND RESID 491:560 )C491 - 560
8X-RAY DIFFRACTION8( CHAIN C AND RESID 561:645 )C561 - 645
9X-RAY DIFFRACTION9( CHAIN H AND RESID 1:125 )H1 - 125
10X-RAY DIFFRACTION10( CHAIN H AND RESID 126:215 )H126 - 215
11X-RAY DIFFRACTION11( CHAIN L AND RESID 1:107 )L1 - 107
12X-RAY DIFFRACTION12( CHAIN L AND RESID 108:213 )L108 - 213

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