[English] 日本語
Yorodumi
- PDB-8w0x: Crystal structure of broadly neutralizing antibody hcab40 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w0x
TitleCrystal structure of broadly neutralizing antibody hcab40 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • Envelope glycoprotein E2
  • hcab40 Fab Heavy Chain
  • hcab40 Fab Light Chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HCV glycoprotein / broadly neutralizing antibodies / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / virion membrane / structural molecule activity / membrane / 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
Similarity search - Domain/homology
Biological speciesHepacivirus hominis
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsFlyak, A.I. / Wilcox, X.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI159822 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI153465 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI153465 United States
CitationJournal: Immunity / Year: 2024
Title: Convergent evolution and targeting of diverse E2 epitopes by human broadly neutralizing antibodies are associated with HCV clearance.
Authors: Ogega, C.O. / Skinner, N.E. / Schoenle, M.V. / Wilcox, X.E. / Frumento, N. / Wright, D.A. / Paul, H.T. / Sinnis-Bourozikas, A. / Clark, K.E. / Figueroa, A. / Bjorkman, P.J. / Ray, S.C. / ...Authors: Ogega, C.O. / Skinner, N.E. / Schoenle, M.V. / Wilcox, X.E. / Frumento, N. / Wright, D.A. / Paul, H.T. / Sinnis-Bourozikas, A. / Clark, K.E. / Figueroa, A. / Bjorkman, P.J. / Ray, S.C. / Flyak, A.I. / Bailey, J.R.
History
DepositionFeb 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Envelope glycoprotein E2
H: hcab40 Fab Heavy Chain
L: hcab40 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,72112
Polymers78,3633
Non-polymers5,3599
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint50 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.911, 79.911, 294.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules C

#1: Protein Envelope glycoprotein E2


Mass: 28946.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus hominis / Plasmid: pCMV / Cell line (production host): HEK293expi / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE15

-
Antibody , 2 types, 2 molecules HL

#2: Antibody hcab40 Fab Heavy Chain


Mass: 25968.047 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): HEK293expi / Production host: Homo sapiens (human)
#3: Antibody hcab40 Fab Light Chain


Mass: 23448.020 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): HEK293expi / Production host: Homo sapiens (human)

-
Sugars , 6 types, 9 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: 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.: 2
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Sodium malonate and 12% PEG 3,350

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.87→40.04 Å / Num. obs: 25984 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.047 / Rrim(I) all: 0.209 / Χ2: 0.84 / Net I/σ(I): 8.9 / Num. measured all: 511303
Reflection shellResolution: 2.87→3.03 Å / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 5.876 / Num. measured all: 76157 / Num. unique obs: 3711 / CC1/2: 0.451 / Rpim(I) all: 1.321 / Rrim(I) all: 6.025 / Χ2: 0.69 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→40.04 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 968 4.77 %
Rwork0.2266 --
obs0.2287 20306 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.12→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 356 0 5284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095429
X-RAY DIFFRACTIONf_angle_d1.2937405
X-RAY DIFFRACTIONf_dihedral_angle_d8.979928
X-RAY DIFFRACTIONf_chiral_restr0.066890
X-RAY DIFFRACTIONf_plane_restr0.01903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.280.34161550.29512686X-RAY DIFFRACTION100
3.28-3.490.34791420.26062700X-RAY DIFFRACTION100
3.49-3.760.28691270.2492708X-RAY DIFFRACTION100
3.76-4.140.28581230.242738X-RAY DIFFRACTION100
4.14-4.730.24091180.21352784X-RAY DIFFRACTION100
4.74-5.960.261580.21562762X-RAY DIFFRACTION100
5.96-40.040.26191450.21662960X-RAY DIFFRACTION100
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)
11.27240.36860.32744.0546-0.43165.0726-0.4118-0.04390.4156-0.02620.1055-0.0069-0.15560.17960.1090.7585-0.3426-0.01061.1759-0.16911.08-84.200215.252-52.9113
25.8679-1.2756-1.27984.10821.22914.32990.32311.2489-0.767-0.3348-0.01280.33180.5928-0.4669-0.06531.3194-0.22370.13711.56-0.19381.0743-70.080113.3193-76.6679
30.9086-1.19310.08943.64440.83994.30060.23390.51610.1849-0.3959-0.1372-0.2562-0.26350.335-0.11880.7245-0.35830.05291.0912-0.03520.8703-72.072122.4588-66.5318
46.8015-2.24523.4023.5233-0.72365.72970.0434-0.3474-0.4687-0.03860.02950.12290.5478-0.5119-0.15450.5898-0.30040.03270.98480.01320.8565-59.82734.8203-40.818
52.92691.4646-0.18323.29251.4153.1158-0.4885-2.0987-0.4647-0.3589-0.517-0.26110.5678-1.16841.0791.1961-0.18850.22222.8765-0.38261.0824-59.5359.278-7.238
65.26493.23624.12216.76482.49895.8516-0.25150.09970.433-0.33240.1642-0.0489-0.45250.49250.18640.5354-0.12330.09691.1104-0.0190.9998-43.35617.723-38.1485
72.39080.61222.21867.0454-1.48033.78020.1973-1.4795-0.47360.302-0.2714-0.60670.5407-1.0647-0.02071.0177-0.3173-0.05882.44150.12981.2005-42.169310.0971-4.539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 413 through 451 )
2X-RAY DIFFRACTION2chain 'C' and (resid 452 through 495 )
3X-RAY DIFFRACTION3chain 'C' and (resid 496 through 645 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 113 )
5X-RAY DIFFRACTION5chain 'H' and (resid 114 through 206 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 107 )
7X-RAY DIFFRACTION7chain 'L' and (resid 108 through 211 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more