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- PDB-6mek: Crystal structure of Hepatitis C virus envelope glycoprotein E2 c... -

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Basic information

Entry
Database: PDB / ID: 6mek
TitleCrystal structure of Hepatitis C virus envelope glycoprotein E2 core in complex with human antibodies HEPC3 and HEPC46
Components
  • E2 GLYCOPROTEIN
  • HEPC3 Heavy Chain
  • HEPC3 Light Chain
  • HEPC46 Heavy Chain
  • HEPC46 Light Chain
KeywordsIMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / transformation of host cell by virus / serine-type peptidase activity / lipid droplet / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / membrane => GO:0016020 ...host cell mitochondrial membrane / host cell lipid droplet / transformation of host cell by virus / serine-type peptidase activity / lipid droplet / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / RNA helicase / cysteine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP binding / cytoplasm
Similarity search - Function
Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / 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 NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / 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 / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Core protein precursor
Similarity search - Component
Biological speciesHepacivirus C
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / 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 / pdbx_validate_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E2 GLYCOPROTEIN
B: HEPC3 Heavy Chain
C: E2 GLYCOPROTEIN
D: HEPC3 Light Chain
E: HEPC46 Light Chain
F: HEPC46 Heavy Chain
G: HEPC46 Light Chain
H: HEPC3 Heavy Chain
I: HEPC46 Heavy Chain
L: HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,91419
Polymers245,20310
Non-polymers4,7109
Water0
1
A: E2 GLYCOPROTEIN
B: HEPC3 Heavy Chain
D: HEPC3 Light Chain
G: HEPC46 Light Chain
I: HEPC46 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5829
Polymers122,6025
Non-polymers1,9814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E2 GLYCOPROTEIN
E: HEPC46 Light Chain
F: HEPC46 Heavy Chain
H: HEPC3 Heavy Chain
L: HEPC3 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,33110
Polymers122,6025
Non-polymers2,7305
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.399, 105.589, 337.280
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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Protein , 1 types, 2 molecules AC

#1: Protein E2 GLYCOPROTEIN


Mass: 25837.098 Da / Num. of mol.: 2 / Mutation: N448D, N576D
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: H2FJ05

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Antibody , 4 types, 8 molecules BHDLEGFI

#2: Antibody HEPC3 Heavy Chain


Mass: 25759.807 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: Antibody HEPC3 Light Chain


Mass: 23384.883 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)
#4: Antibody HEPC46 Light Chain


Mass: 22938.188 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)
#5: Antibody HEPC46 Heavy Chain


Mass: 24681.619 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)

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Sugars , 5 types, 9 molecules

#6: 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
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
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
#7: 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
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
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
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 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)
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: 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
#10: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.05 % / Mosaicity: 0.45 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.02 M Nickel(II) chloride hexahydrate, 0.02 M magnesium chloride hexahydrate, 0.02 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate pH 4.5, 24% PEG 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→89.49 Å / Num. obs: 60807 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 77.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.052 / Rrim(I) all: 0.168 / Net I/σ(I): 10.7 / Num. measured all: 617678 / Scaling rejects: 683
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-2.988.21.63243670.4110.5931.74599.6
12.97-89.4910.60.0488070.9990.0150.05199.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 3.1→76.967 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.58
RfactorNum. reflection% reflection
Rfree0.2899 2479 4.97 %
Rwork0.2232 --
obs0.2265 49898 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.86 Å2 / Biso mean: 76.8476 Å2 / Biso min: 32.64 Å2
Refinement stepCycle: final / Resolution: 3.1→76.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15435 0 312 0 15747
Biso mean--109.54 --
Num. residues----2044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.15960.41671280.309226252753
3.1596-3.22410.29521130.289425822695
3.2241-3.29420.38131420.27725942736
3.2942-3.37090.31591460.250625442690
3.3709-3.45520.33871260.255925952721
3.4552-3.54860.31061450.246826122757
3.5486-3.6530.37231640.247525632727
3.653-3.77090.34661460.252226392785
3.7709-3.90570.31791210.251626092730
3.9057-4.06210.35211290.235826252754
4.0621-4.24690.29071180.206326252743
4.2469-4.47080.24631380.186526502788
4.4708-4.75090.21131320.182226242756
4.7509-5.11760.25561430.182826382781
5.1176-5.63250.27731420.191226592801
5.6325-6.44720.26911520.22126722824
6.4472-8.12130.31981350.224727272862
8.1213-76.99020.24241590.225828362995

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