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- PDB-8qp7: Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 4... -

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Basic information

Entry
Database: PDB / ID: 8qp7
TitleCrystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04
ComponentsYop effector YopM,Internalin B
KeywordsSTRUCTURAL PROTEIN / Scaffold design / HCV Immunogen / Complex
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) ...: / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Internalin B / Yop effector YopM
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNagarathinam, K. / Cramer, J.T. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KR 2880 / 3-1 Germany
CitationJournal: To Be Published
Title: Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04
Authors: Nagarathinam, K. / Krey, T. / Scheck, A. / Labuhn, M. / Stroeh, L.J. / Herold, E. / Veselkova, B. / Cramer, J.T. / Rosset, S. / Vollers, S.S. / Bankwitz, D. / Ballmaier, M. / Boening, H. / ...Authors: Nagarathinam, K. / Krey, T. / Scheck, A. / Labuhn, M. / Stroeh, L.J. / Herold, E. / Veselkova, B. / Cramer, J.T. / Rosset, S. / Vollers, S.S. / Bankwitz, D. / Ballmaier, M. / Boening, H. / Roth, E. / Khera, T. / Ahsendorf, H. / Tune, S. / Dittrich-Breiholz, O. / Obleser, J. / Nassal, M. / Jaeck, H.M. / Pietschmann, T. / Correia, B.E.
History
DepositionSep 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Yop effector YopM,Internalin B


Theoretical massNumber of molelcules
Total (without water)33,0691
Polymers33,0691
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.290, 31.670, 135.750
Angle α, β, γ (deg.)90.000, 94.314, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Yop effector YopM,Internalin B / 4CIL_04


Mass: 33068.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein sequence is an insilico designed sequence using PDB ID 4CIL as the template which harbors one of the glycoprotein epitopes of HCV.
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yopM, inlB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74988, UniProt: P0DQD2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 25% (w/v) PEG 1500, 100 mM MMT buffer pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.999995 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 2.05→30.06 Å / Num. obs: 16198 / % possible obs: 97.23 % / Redundancy: 4.5 % / Biso Wilson estimate: 30.83 Å2 / CC1/2: 0.98 / CC star: 0.995 / Net I/σ(I): 9.85
Reflection shellResolution: 2.05→2.123 Å / Mean I/σ(I) obs: 2.54 / Num. unique obs: 1652 / CC1/2: 0.323 / % possible all: 95.02

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
Coot1.19_4092model building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30.06 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2617 807 5.03 %
Rwork0.2144 15239 -
obs0.2168 16046 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.75 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 0 127 2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172119
X-RAY DIFFRACTIONf_angle_d0.46842887
X-RAY DIFFRACTIONf_chiral_restr0.0409349
X-RAY DIFFRACTIONf_plane_restr0.0038371
X-RAY DIFFRACTIONf_dihedral_angle_d4.3280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.180.29821320.24782468X-RAY DIFFRACTION95.87
2.18-2.350.31261340.25112516X-RAY DIFFRACTION97.53
2.35-2.580.32941340.25022538X-RAY DIFFRACTION97.77
2.58-2.960.33571340.24852547X-RAY DIFFRACTION98.42
2.96-3.720.24461360.20092573X-RAY DIFFRACTION98.19
3.72-30.060.21281370.1882597X-RAY DIFFRACTION95.86
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)
10.0396583038042-0.00234491686741-0.02634530734460.09405427381720.01767972065430.02046228156760.1215603095090.0269247888451-0.1609650314070.07222307981890.0734967933592-0.1294546593630.1089227813920.1584036757350.7708180662650.454606056034-0.0780839638717-0.2305728082070.78324216063-0.06073519693340.39506146995722.64591507194.8723995241961.1709370148
20.106032780901-0.113429176864-0.02412098980620.447169110162-0.07100128173920.03455652464120.117166260171-0.485214823374-0.05059498831940.0462322080256-0.1368569177870.218722377128-0.2082475379550.2090987651470.005998941441380.332829550805-0.121786299468-0.02090064523070.717299225581-0.03242560125760.29041307494810.28382288622.2229406927961.8685494219
30.0853258594243-0.0143571433934-0.1043988064080.08127463889210.03244277976730.185469016117-0.0856171267428-0.482553355622-0.1275424113480.427957284078-0.0567533804860.0916204095858-0.2004663128920.034316153684-0.002783420145310.301160265845-0.04904463875340.01487146304850.539506602219-0.03594550242090.32948279522712.83923903964.8758657855352.3810060844
40.09832044425730.0279828893840.1211049705710.06423449505180.05847699294050.161994137521-0.04767210487070.1313433706380.1038996840350.04232748979610.0821982342472-0.2424966675640.07588253940090.08508252866550.001090932779040.278215573743-0.00701424603974-0.01906885670960.462437484084-0.04666926798150.33667281790511.42291729920.91517216702246.323470159
50.4084653212170.05557059728910.3993737908180.1892471711430.2239796701280.5466006875370.0548040246909-0.154393127212-0.0143527221834-0.0254198430995-0.0383307089840.05523670998590.0004547378124950.0712304689619-0.0001102043875540.231617462090.002688030414760.03270056950380.256045329469-0.03742271743310.344595416074.679828365793.0483157307133.1948498153
60.324404215484-0.2375178884130.0310503361570.2018237205250.009662474858130.5221713591820.07005440829030.09984555823090.0660974022745-0.0372317344817-0.0322158669844-0.0096427559287-0.0810660341856-0.03449684191959.72658295908E-50.301529128280.006874776880.007090778723030.229949349009-0.0379507078590.30647185554-1.9388935486816.778500398916.1432376523
70.376412644468-0.3152212176390.1102182705280.265565002599-0.07044485155330.2908601005690.1504849549790.03361705059290.1472184131870.0500864517907-0.1454968140180.126733824376-0.3321285224520.08588369429650.0002946061399910.337913916882-0.0214947643596-0.0002080271041370.219297799456-0.01432910313890.393174851421-1.713173460722.455225666514.3016484859
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 29 )8 - 291 - 19
22chain 'A' and (resid 30 through 49 )30 - 4920 - 39
33chain 'A' and (resid 50 through 80 )50 - 8040 - 66
44chain 'A' and (resid 81 through 102 )81 - 10267 - 88
55chain 'A' and (resid 103 through 190 )103 - 19089 - 176
66chain 'A' and (resid 191 through 243 )191 - 243177 - 229
77chain 'A' and (resid 244 through 288 )244 - 288230 - 274

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