[English] 日本語
Yorodumi
- PDB-7rfc: Crystal structure of broadly neutralizing antibody mAb1382 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rfc
TitleCrystal structure of broadly neutralizing antibody mAb1382 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • envelope glycoprotein E2
  • mAb1382 Heavy Chain
  • mAb1382 Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 speciesHomo sapiens (human)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsFlyak, A.I. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127469 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI153465 United States
CitationJournal: Immunity / Year: 2022
Title: Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization.
Authors: Weber, T. / Potthoff, J. / Bizu, S. / Labuhn, M. / Dold, L. / Schoofs, T. / Horning, M. / Ercanoglu, M.S. / Kreer, C. / Gieselmann, L. / Vanshylla, K. / Langhans, B. / Janicki, H. / Stroh, L. ...Authors: Weber, T. / Potthoff, J. / Bizu, S. / Labuhn, M. / Dold, L. / Schoofs, T. / Horning, M. / Ercanoglu, M.S. / Kreer, C. / Gieselmann, L. / Vanshylla, K. / Langhans, B. / Janicki, H. / Stroh, L.J. / Knops, E. / Nierhoff, D. / Spengler, U. / Kaiser, R. / Bjorkman, P.J. / Krey, T. / Bankwitz, D. / Pfeifer, N. / Pietschmann, T. / Flyak, A.I. / Klein, F.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mAb1382 Heavy Chain
B: mAb1382 Light Chain
C: envelope glycoprotein E2
D: envelope glycoprotein E2
H: mAb1382 Heavy Chain
L: mAb1382 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,87519
Polymers155,5226
Non-polymers5,35313
Water00
1
A: mAb1382 Heavy Chain
B: mAb1382 Light Chain
C: envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0639
Polymers77,7613
Non-polymers2,3026
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-14 kcal/mol
Surface area31130 Å2
MethodPISA
2
D: envelope glycoprotein E2
H: mAb1382 Heavy Chain
L: mAb1382 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,81210
Polymers77,7613
Non-polymers3,0517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-3 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.291, 140.184, 142.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 225)
21(chain H and (resid 2 through 144 or resid 146 through 225))
12(chain B and resid 1 through 214)
22chain L
13(chain C and (resid 421 through 475 or resid 484...
23(chain D and (resid 421 through 448 or resid 452...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 2 through 225)A2 - 225
211(chain H and (resid 2 through 144 or resid 146 through 225))H2 - 144
221(chain H and (resid 2 through 144 or resid 146 through 225))H146 - 225
112(chain B and resid 1 through 214)B1 - 214
212chain LL1 - 212
113(chain C and (resid 421 through 475 or resid 484...C421 - 475
123(chain C and (resid 421 through 475 or resid 484...C484 - 645
133(chain C and (resid 421 through 475 or resid 484...C4231 - 5562
143(chain C and (resid 421 through 475 or resid 484...C6231
213(chain D and (resid 421 through 448 or resid 452...D421 - 448
223(chain D and (resid 421 through 448 or resid 452...D452 - 475
233(chain D and (resid 421 through 448 or resid 452...D484 - 571
243(chain D and (resid 421 through 448 or resid 452...D576 - 645
253(chain D and (resid 421 through 448 or resid 452...D4231 - 5401
263(chain D and (resid 421 through 448 or resid 452...D5562

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 2 molecules CD

#3: Protein envelope glycoprotein E2


Mass: 28946.479 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 214-475)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Plasmid: pCMV / Cell line (production host): HEK293expi / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE26

-
Antibody , 2 types, 4 molecules AHBL

#1: Antibody mAb1382 Heavy Chain


Mass: 24965.896 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): HEK293expi / Production host: Homo sapiens (human)
#2: Antibody mAb1382 Light Chain


Mass: 23848.504 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): HEK293expi / Production host: Homo sapiens (human)

-
Sugars , 4 types, 13 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.: 7
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-(1-3)-[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-(1-4)-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]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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: obtained synthetically / 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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.35 % / Mosaicity: 1.07 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.03 M citric acid, 0.07 M Bis-Tris propane, pH 7.6, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.24→83.67 Å / Num. obs: 33598 / % possible obs: 99.1 % / Redundancy: 5.2 % / CC1/2: 0.911 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.136 / Rrim(I) all: 0.312 / Net I/σ(I): 4 / Num. measured all: 174067 / Scaling rejects: 1430
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
3.24-3.45.11.1912269044150.4580.5721.3261.599.2
10.75-83.675.20.069526710190.9950.0320.0766.798.1

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6MEH & 6MEI

6meh

6mei


Resolution: 3.24→52.15 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 1813 5.44 %
Rwork0.2329 31520 -
obs0.2358 33333 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.85 Å2 / Biso mean: 72.5916 Å2 / Biso min: 35.32 Å2
Refinement stepCycle: final / Resolution: 3.24→52.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10010 0 352 0 10362
Biso mean--104.49 --
Num. residues----1304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1300X-RAY DIFFRACTION10.036TORSIONAL
12H1300X-RAY DIFFRACTION10.036TORSIONAL
21B1298X-RAY DIFFRACTION10.036TORSIONAL
22L1298X-RAY DIFFRACTION10.036TORSIONAL
31C1398X-RAY DIFFRACTION10.036TORSIONAL
32D1398X-RAY DIFFRACTION10.036TORSIONAL
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 (%)
3.24-3.330.321330.3012388252198
3.33-3.430.39521230.322420254399
3.43-3.540.43781140.35782360247496
3.54-3.660.40051520.32572404255699
3.66-3.810.3731590.33612349250897
3.81-3.980.43031300.35662361249196
3.98-4.190.27341340.217424572591100
4.19-4.450.22451600.18112406256699
4.45-4.80.22171150.16522429254498
4.8-5.280.20321310.16372465259699
5.28-6.040.24391680.18082435260399
6.04-7.610.23771360.21232493262999
7.61-52.150.24051580.18642553271197
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)
13.1390.8155-0.88813.7947-2.69084.113-0.0829-0.54760.32470.38910.26710.7226-0.2411-0.1918-0.18840.42740.10530.05490.49660.01650.624-4.613-7.33455.103
23.7288-1.38181.06911.62030.09654.6353-0.24630.091-0.35090.42960.36310.6710.1427-0.3265-0.09740.5776-0.04540.08430.33390.11280.7411-3.877-15.45557.572
31.58921.5575-1.32844.7776-2.93534.19310.18790.00470.26750.4071-0.1967-0.0524-0.4158-0.29150.03360.41390.08560.02150.3205-0.0190.50037.912.72528.027
45.04440.2836-2.36471.7444-0.61871.7979-0.33940.545-0.10960.03360.19710.2528-0.142-0.10030.14230.38710.0311-0.0720.29330.02970.567927.51927.768-0.328
54.36821.5442-1.54182.7128-1.01134.9166-0.07690.1248-0.51170.038-0.421-0.38040.42580.72150.53880.44490.08550.03130.41450.1680.669327.0042.25227.856
65.1469-1.27261.45457.1087-1.08114.6017-0.3834-0.48040.17980.23040.2264-0.0877-0.78670.23860.17130.3843-0.009-0.02960.46360.00470.519437.5831.54211.971
73.4063-0.6031.55865.12233.58934.93750.55141.55211.0080.330.0816-0.5234-0.64370.6371-0.34150.6810.0870.17440.8525-0.0161.07081.898-5.652-8.096
83.1775-0.8433-0.9950.22140.26340.3340.0123-0.39411.4958-0.80540.43870.133-0.84050.0592-0.23611.090.0182-0.14550.6169-0.05920.5229-7.265-3.758-16.985
94.52010.6506-1.15313.71171.41086.60360.0231.11170.5635-1.18040.8431-0.48920.24581.1985-0.99640.972-0.14620.1591.1405-0.22240.6667.503-17.56-30.295
104.20270.5613-0.93262.02251.54561.89-0.07410.1733-0.0617-0.28460.2787-0.36760.29550.5648-0.19740.82240.14510.01330.7426-0.06460.45562.576-21.013-19.813
113.26150.0961-0.18042.70790.89973.4160.0253-0.1707-0.49030.1176-0.32360.56530.3029-0.35030.31540.48060.0082-0.04440.4288-0.04740.6804-26.3170.0828.197
125.64711.5532-0.92695.1599-1.25443.07340.0952-0.05850.44120.36620.13840.3152-0.2541-0.3649-0.20110.37430.03270.10340.3933-0.02420.4215-33.62931.38321.574
132.0154-1.1083-0.33925.42695.18475.3873-0.00730.1078-0.024-0.74480.08720.0243-0.4057-0.0172-0.11060.5376-0.04650.01970.46710.12580.414-6.2078.1547.135
146.84271.1443-4.79423.2970.7965.9833-0.1193-1.05490.01340.7699-0.0388-0.3079-0.20030.350.20910.61310.0514-0.07390.51820.07680.4139-23.95928.35734.356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 421:526 )D421 - 526
2X-RAY DIFFRACTION2( CHAIN D AND RESID 527:645 )D527 - 645
3X-RAY DIFFRACTION3( CHAIN H AND RESID 2:124 )H2 - 124
4X-RAY DIFFRACTION4( CHAIN H AND RESID 125:214 )H125 - 214
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:109 )L1 - 109
6X-RAY DIFFRACTION6( CHAIN L AND RESID 110:212 )L110 - 212
7X-RAY DIFFRACTION7( CHAIN C AND RESID 421:436 )C421 - 436
8X-RAY DIFFRACTION8( CHAIN C AND RESID 437:455 )C437 - 455
9X-RAY DIFFRACTION9( CHAIN C AND RESID 456:501 )C456 - 501
10X-RAY DIFFRACTION10( CHAIN C AND RESID 502:645 )C502 - 645
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:109 )B1 - 109
12X-RAY DIFFRACTION12( CHAIN B AND RESID 110:213 )B110 - 213
13X-RAY DIFFRACTION13( CHAIN A AND RESID 1:124 )A1 - 124
14X-RAY DIFFRACTION14( CHAIN A AND RESID 125:215 )A125 - 215

+
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://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