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- PDB-8dk6: Structure of hepatitis C virus envelope N-terminal truncated glyc... -

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Basic information

Entry
Database: PDB / ID: 8dk6
TitleStructure of hepatitis C virus envelope N-terminal truncated glycoprotein 2 (E2) (residues 456-713) from J6 genotype
Components
  • 2A12 Fab Heavy chain
  • 2A12 Fab light chain
  • Envelope glycoprotein E2
KeywordsVIRAL PROTEIN / Hepatitis C virus glycoprotein 2 (E2)
Function / homology
Function and homology information


host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / symbiont entry into host cell / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / 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 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / DEAD box, Flavivirus / Flavivirus DEAD 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHepatitis C virus isolate HC-J6
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKumar, A. / Rohe, T. / Elrod, E.J. / Khan, A.G. / Dearborn, A.D. / Kissinger, R. / Grakoui, A. / Marcotrigiano, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2023
Title: Regions of hepatitis C virus E2 required for membrane association.
Authors: Kumar, A. / Rohe, T.C. / Elrod, E.J. / Khan, A.G. / Dearborn, A.D. / Kissinger, R. / Grakoui, A. / Marcotrigiano, J.
History
DepositionJul 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope glycoprotein E2
H: 2A12 Fab Heavy chain
L: 2A12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3424
Polymers76,9183
Non-polymers4241
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.970, 125.540, 157.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Envelope glycoprotein E2


Mass: 29111.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus isolate HC-J6 / Cell (production host): Gnti- HEK293 produced / Cell line (production host): Mammalian cell-line / Production host: Homo sapiens (human) / References: UniProt: A0A2I6PIY1
#2: Antibody 2A12 Fab Heavy chain


Mass: 23462.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hyridoma / Production host: Homo sapiens (human)
#3: Antibody 2A12 Fab light chain


Mass: 24343.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hyridoma / Production host: Homo sapiens (human)
#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.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 8.3, Cryoprotectant used 30% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→48.97 Å / Num. obs: 35577 / % possible obs: 97.8 % / Redundancy: 4 % / Biso Wilson estimate: 39.1 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.062 / Net I/σ(I): 8.8
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5166 / CC1/2: 0.571 / Rpim(I) all: 0.334 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
iMOSFLM7.0.077data reduction
SCALA7.0.077data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WEB

4web


Resolution: 2.45→48.39 Å / SU ML: 0.2762 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.774 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 3268 5.04 %
Rwork0.2031 61617 -
obs0.2046 35524 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 28 180 4604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284549
X-RAY DIFFRACTIONf_angle_d0.68226221
X-RAY DIFFRACTIONf_chiral_restr0.0446705
X-RAY DIFFRACTIONf_plane_restr0.0051788
X-RAY DIFFRACTIONf_dihedral_angle_d3.25252673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.30881450.28122648X-RAY DIFFRACTION95.13
2.49-2.530.2911430.27612667X-RAY DIFFRACTION94.87
2.53-2.570.33121380.26332776X-RAY DIFFRACTION95.14
2.57-2.610.29941530.26622665X-RAY DIFFRACTION94.91
2.61-2.660.31541380.27072665X-RAY DIFFRACTION94.63
2.66-2.710.27671430.26412721X-RAY DIFFRACTION94.52
2.71-2.770.23021270.25492688X-RAY DIFFRACTION94.78
2.77-2.830.27341390.2452668X-RAY DIFFRACTION95.06
2.83-2.890.25451240.23012760X-RAY DIFFRACTION93.61
2.89-2.960.27721490.22462583X-RAY DIFFRACTION92.8
2.96-3.040.25271330.21162636X-RAY DIFFRACTION91.93
3.04-3.130.26831300.22112696X-RAY DIFFRACTION94.96
3.13-3.230.23311340.222793X-RAY DIFFRACTION96.12
3.23-3.350.2281270.22772685X-RAY DIFFRACTION95.94
3.35-3.480.2921390.21242749X-RAY DIFFRACTION95.03
3.48-3.640.2511340.20042664X-RAY DIFFRACTION94.53
3.64-3.830.26261690.18862668X-RAY DIFFRACTION93.97
3.83-4.070.17091340.17462660X-RAY DIFFRACTION92.98
4.07-4.390.18291120.15862622X-RAY DIFFRACTION91.47
4.39-4.830.15731700.15012627X-RAY DIFFRACTION93.3
4.83-5.530.17751660.15752632X-RAY DIFFRACTION94.24
5.53-6.960.23111780.20762708X-RAY DIFFRACTION95.78
6.96-48.390.23631430.19912636X-RAY DIFFRACTION93.07
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)
11.98701419382-0.6997714499250.3292693286685.32365742061-0.9351463918270.906632118951-0.062851098798-0.1257089014880.07174984499570.07311071960630.234674273582-0.1887602726780.040858795635-0.289915118278-0.1290796963610.263930298285-0.00326931053963-0.0003528727742020.328429928334-0.06201096026950.49458434781846.443-9.46534.33
21.49432900674-2.97221787413-1.005129293835.889834604442.006274130360.988434164245-0.02266484079-0.1658444449380.2389877220210.373713066189-0.04943863972630.6721137782620.192201331059-0.2410409295270.2217060442110.266983985668-0.07843713235280.01483680270550.425275576657-0.05583869308570.67626492587437.892-12.21835.476
33.51172843773-2.31122399102-1.218525140162.471186293740.2136355910791.37457471921-0.08911081255080.07323508141590.1117335502870.09537375203990.189579242353-0.452643343132-0.1410137470550.269742951403-0.07216434961750.301638967342-0.0212638063066-0.03689935734640.372381429742-0.02928550902990.56442594017365.47817.50545.585
40.09107957598370.4734685854190.4687550405592.568595205741.201946345581.464594948290.07515095098490.0602511786219-0.0567880238766-0.06830680694880.0362413966333-0.2472693735220.0708373636704-0.0130828817225-0.1058113432670.244385535015-0.02144380529970.04324823148510.3790032523540.009247077423150.58654676209757.283-0.31931.139
53.54172414591.641419177281.48276716993.075918924411.113135690852.96005387369-0.1943859963570.5697357373060.160968919262-0.628373436910.275507813779-0.15099071751-0.001777070355120.347188525565-0.09187417853820.411889805612-0.01412643151350.1089133305280.338176457791-0.05259419003710.54284231879752.796-12.35318.345
68.027448551022.062436324631.771360477483.570161966434.235673112955.088373296150.3290369088290.4936985444221.248643601260.6105186299050.672216907313-0.105914465034-1.575007632760.211772397601-0.9217112908251.11303689531-0.00523435872583-0.04862410130120.6385927943010.2320723427750.80924343876550.69110.74289.1
72.310028095050.04349192850130.9940754211765.3988237424-3.819266794096.900859309150.15459267152-0.356163262998-0.03665862900140.8431306159380.3432904134770.752102663707-0.710097691196-1.0524113654-0.4479363513690.5655709964110.09767846811040.1190131288450.5531152172410.1134797299610.58439181475240.9044.16785.847
86.27114141373-2.83368047306-0.5331401979769.089625602890.03775814138847.847432566680.180098071546-0.1666796605460.1309266888470.601690254228-0.080765154170.428574706096-0.522590982067-0.727177710572-0.1313867269590.6424156756280.0170298838352-0.02411630426440.357329026060.07536078704880.44110155735248.90810.69782.696
97.97226265862-3.920664267771.758761268617.847537074793.747235094274.84338214177-0.111221758388-0.588930974545-1.397441034140.5842047185780.054527860092-0.669164185025-1.086495894321.047302549580.1163596852860.777841566737-0.0992012792276-0.07862829381730.551364952690.1903467028620.75958149506857.77314.18580.268
106.57215115042-1.786854404973.232656528913.415767955831.673016385055.30595923185-0.143528658039-0.526842248813-0.4686712651090.7644230683330.480383310774-0.120164166901-0.7426776666160.14588630415-0.3384829608920.7973411074110.02441326600180.009754154940760.4397165918550.05430678921550.45713487439151.09820.73575.651
112.284218525810.09020288820820.1440630780514.966914135-0.9784498116536.39647188117-0.352669560478-0.41368318962-0.4846818631921.28423131518-0.01479437538330.902966794755-1.13630829611-0.2271322259940.1818128502280.6849657360780.1203940313260.03231914875590.35401689440.09292094929460.46637153625348.65722.92571.968
121.570474869491.37559325181.331617164411.557854069921.994266826763.05789126166-0.460883976566-0.0511169045628-0.237515130580.6157780515750.464319170819-0.254839252457-0.07262159939450.192876479763-0.1117173908070.5661619052010.0660275025046-0.05307647340710.3247425327150.1153507091180.46769492285753.27520.50268.776
130.9966111210050.6920876217612.868047090173.38825176233-0.116104396539.625592395150.005268895291270.203143141024-0.3518957226270.1567934843610.1848133615990.1581573508340.130841930903-0.2369469719140.0121057987140.169752087177-0.008648613434460.09535313932240.3380628410070.02507898657830.61315674278238.66310.84442.604
142.090699023390.6078232008930.389073122743.187485598430.9990200455835.05802181309-0.0315648467125-0.179264860186-0.1436765162060.1462451537960.05435257361420.153168314801-0.1759967559580.168078799325-0.05267096217320.186358533970.04614369148730.04287560916580.2453585959740.02385063586890.4108427310744.43318.83548.965
156.291356214641.04535506434-0.7412068775695.89284594502-3.303452878585.382112668820.2045524282890.006169599942760.6531864000830.1900854793270.1902653675220.673118544508-0.358548968027-0.135790282015-0.3793843832670.2830494044470.03011440437220.02706979771670.313372948997-0.06652394131380.62179727420837.96421.31747.591
160.2012720922970.0606977568960.1680006714771.662970461760.5447782525980.8719757856220.007334626012390.0758074982261-0.136571295574-0.0549721710174-0.05797550314710.00529100092740.0156484981166-0.02392850411530.04808294618130.193275357055-0.03128615929160.03182531657120.329496879077-0.02368337283870.43471712385744.3822.47636.348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 151:199 )H151 - 199
2X-RAY DIFFRACTION2( CHAIN H AND RESID 200:219 )H200 - 219
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:81 )L1 - 81
4X-RAY DIFFRACTION4( CHAIN L AND RESID 82:155 )L82 - 155
5X-RAY DIFFRACTION5( CHAIN L AND RESID 156:218 )L156 - 218
6X-RAY DIFFRACTION6( CHAIN E AND RESID 491:500 )E491 - 500
7X-RAY DIFFRACTION7( CHAIN E AND RESID 501:540 )E501 - 540
8X-RAY DIFFRACTION8( CHAIN E AND RESID 541:562 )E541 - 562
9X-RAY DIFFRACTION9( CHAIN E AND RESID 563:601 )E563 - 601
10X-RAY DIFFRACTION10( CHAIN E AND RESID 602:617 )E602 - 617
11X-RAY DIFFRACTION11( CHAIN E AND RESID 618:637 )E618 - 637
12X-RAY DIFFRACTION12( CHAIN E AND RESID 638:652 )E638 - 652
13X-RAY DIFFRACTION13( CHAIN H AND RESID 1:17 )H1 - 17
14X-RAY DIFFRACTION14( CHAIN H AND RESID 18:60 )H18 - 60
15X-RAY DIFFRACTION15( CHAIN H AND RESID 61:83 )H61 - 83
16X-RAY DIFFRACTION16( CHAIN H AND RESID 84:150 )H84 - 150

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