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- PDB-4uoi: Unexpected structure for the N-terminal domain of Hepatitis C vir... -

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Basic information

Entry
Database: PDB / ID: 4uoi
TitleUnexpected structure for the N-terminal domain of Hepatitis C virus envelope glycoprotein E1
ComponentsGENOME POLYPROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell lipid droplet / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Hepatitis C virus envelope glycoprotein E1, chain C / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHEPATITIS C VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.49 Å
AuthorsEl Omari, K. / Iourin, O. / Kadlec, J. / Harlos, K. / Grimes, J.M. / Stuart, D.I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Unexpected Structure for the N-Terminal Domain of Hepatitis C Virus Envelope Glycoprotein E1
Authors: El Omari, K. / Iourin, O. / Kadlec, J. / Fearn, R. / Hall, D.R. / Harlos, K. / Grimes, J.M. / Stuart, D.I.
#1: Journal: Nat.Commun. / Year: 2014
Title: Unexpected Structure for the N-Terminal Domain of Hepatitis C Virus Envelope Glycoprotein E1.
Authors: El Omari, K. / Iourin, O. / Kadlec, J. / Sutton, G. / Harlos, K. / Grimes, J.M. / Stuart, D.I.
History
DepositionJun 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references / Other
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENOME POLYPROTEIN
B: GENOME POLYPROTEIN
C: GENOME POLYPROTEIN
D: GENOME POLYPROTEIN
E: GENOME POLYPROTEIN
F: GENOME POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,91316
Polymers57,7006
Non-polymers2,21210
Water00
1
A: GENOME POLYPROTEIN
C: GENOME POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6764
Polymers19,2332
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-15.3 kcal/mol
Surface area8360 Å2
MethodPISA
2
D: GENOME POLYPROTEIN
E: GENOME POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1186
Polymers19,2332
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-11.3 kcal/mol
Surface area10600 Å2
MethodPISA
3
B: GENOME POLYPROTEIN
hetero molecules

F: GENOME POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1186
Polymers19,2332
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z+1/41
Buried area4320 Å2
ΔGint-7.8 kcal/mol
Surface area11350 Å2
MethodPISA
4
F: GENOME POLYPROTEIN
hetero molecules

B: GENOME POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1186
Polymers19,2332
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Unit cell
Length a, b, c (Å)105.006, 105.006, 204.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
GENOME POLYPROTEIN / HCV E1


Mass: 9616.738 Da / Num. of mol.: 6 / Fragment: N-TERMINAL DOMAIN, RESIDUES 16-94 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEPATITIS C VIRUS / Strain: H77 / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: H9XGD6
#2: 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.: 10
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
Has protein modificationY

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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: 4.89 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growpH: 4.8
Details: 15% (WT/V) PEG 1500, 3.6% (WT/V) PEG 4000 AND 0.05 M SODIUM ACETATE PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 15137 / % possible obs: 99.5 % / Observed criterion σ(I): 2.2 / Redundancy: 6.2 % / Biso Wilson estimate: 88.43 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.6
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.49→31.29 Å / Cor.coef. Fo:Fc: 0.9158 / Cor.coef. Fo:Fc free: 0.9182 / SU R Cruickshank DPI: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.972 / SU Rfree Blow DPI: 0.385 / SU Rfree Cruickshank DPI: 0.386
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 762 5.05 %RANDOM
Rwork0.213 ---
obs0.2144 15078 99.1 %-
Displacement parametersBiso mean: 117.45 Å2
Baniso -1Baniso -2Baniso -3
1--6.4586 Å20 Å20 Å2
2---6.4586 Å20 Å2
3---12.9172 Å2
Refine analyzeLuzzati coordinate error obs: 0.925 Å
Refinement stepCycle: LAST / Resolution: 3.49→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 140 0 3212
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164515HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1481SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes495HARMONIC5
X-RAY DIFFRACTIONt_it3293HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion3.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion460SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3559SEMIHARMONIC4
LS refinement shellResolution: 3.49→3.73 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2148 125 4.8 %
Rwork0.2283 2479 -
all0.2276 2604 -
obs--99.1 %
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)
110.0118-0.9478-5.17220.6239-0.14792.1947-0.0010.0179-0.2127-0.2280.05060.0327-0.16510.0294-0.0496-0.09180.2792-0.07430.0975-0.2566-0.022439.971810.1625-150.196
20.6899-0.29321.53832.45481.25954.50470.00240.0902-0.13010.25420.0524-0.0837-0.17920.2848-0.05480.023-0.13370.0217-0.046-0.0155-0.061858.296512.9128-128.416
37.2464-5.2921.31986.3565-1.42095.25830.02460.05670.1561-0.0689-0.03990.04850.00720.25880.0153-0.13110.17940.04660.1292-0.02130.010938.80718.1808-143.581
45.99032.23933.14973.17220.99771.0693-0.0424-0.0050.12570.21480.1788-0.0684-0.33070.2526-0.13630.07480.1485-0.304-0.0017-0.2599-0.021190.8562-6.2138-158.076
52.6722-1.5258-1.9133.46591.86062.1832-0.0106-0.2626-0.01530.27190.14920.07520.01760.0556-0.1387-0.03460.304-0.1197-0.031-0.12140.04379.6992-8.4191-151.701
60.8451.41460.91381.1999-1.80832.91960.0338-0.0476-0.0118-0.1154-0.05150.083-0.2728-0.08450.01770.08310.069-0.02370.0261-0.0708-0.084965.10532.4391-170.619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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