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- PDB-2ch8: Structure of the Epstein-Barr Virus Oncogene BARF1 -

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Basic information

Entry
Database: PDB / ID: 2ch8
TitleStructure of the Epstein-Barr Virus Oncogene BARF1
Components33 KDA EARLY PROTEIN
KeywordsVIRAL PROTEIN / BARF1 / IMMUNOGLOBULIN DOMAIN / ONCOGENE / EARLY PROTEIN
Function / homology
Function and homology information


extracellular region / identical protein binding
Similarity search - Function
Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Secreted protein BARF1
Similarity search - Component
Biological speciesEPSTEIN-BARR VIRUS (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsTarbouriech, N. / Ruggiero, F. / deTurenne-Tessier, M. / Ooka, T. / Burmeister, W.P.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the Epstein-Barr Virus Oncogene Barf1
Authors: Tarbouriech, N. / Ruggiero, F. / Deturenne-Tessier, M. / Ooka, T. / Burmeister, W.P.
History
DepositionMar 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 33 KDA EARLY PROTEIN
B: 33 KDA EARLY PROTEIN
C: 33 KDA EARLY PROTEIN
D: 33 KDA EARLY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,56220
Polymers89,8744
Non-polymers4,68716
Water9,602533
1
A: 33 KDA EARLY PROTEIN
D: 33 KDA EARLY PROTEIN
hetero molecules

A: 33 KDA EARLY PROTEIN
D: 33 KDA EARLY PROTEIN
hetero molecules

A: 33 KDA EARLY PROTEIN
D: 33 KDA EARLY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,84230
Polymers134,8126
Non-polymers7,03124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
2
B: 33 KDA EARLY PROTEIN
C: 33 KDA EARLY PROTEIN
hetero molecules

B: 33 KDA EARLY PROTEIN
C: 33 KDA EARLY PROTEIN
hetero molecules

B: 33 KDA EARLY PROTEIN
C: 33 KDA EARLY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,84230
Polymers134,8126
Non-polymers7,03124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)179.245, 179.245, 95.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
33 KDA EARLY PROTEIN / BARF1 / P33


Mass: 22468.619 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EPSTEIN-BARR VIRUS (Epstein-Barr virus)
Strain: B95-8 / Cell line (production host): HELA / Production host: HOMO SAPIENS (human) / References: UniProt: P03228
#2: Polysaccharide
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Pt
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-21 SIGNAL PEPTIDE, CLEAVED.

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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: 3.15 Å3/Da / Density % sol: 60 %
Crystal growpH: 6
Details: 1 M AMMONIUM SULPHATE,1-2 % PEG 3350,100 MM BISTRIS/HCL PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 50910 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.98 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2583 5.1 %RANDOM
Rwork0.174 ---
obs0.177 48327 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.32 Å20 Å2
2---0.64 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5958 0 168 533 6659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2011.9598620
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0495738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4523.116276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.968151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8761533
X-RAY DIFFRACTIONr_chiral_restr0.1630.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024693
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3010.22642
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.290
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.53851
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70926065
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68732868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.794.52555
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 206
Rwork0.185 3555
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)
13.02571.0131.03812.53710.88551.785-0.03990.15360.0286-0.1098-0.0020.2186-0.02250.04910.042-0.18980.02780.0127-0.09390.0053-0.172749.77251.9561-0.1789
24.25412.77160.45431.89360.1920.1717-0.15790.2170.4604-0.38450.14470.1919-0.1444-0.04540.0132-0.0537-0.0386-0.0037-0.0320.03390.08673.819385.46843.4354
33.7451-0.3572-0.1631.8673-0.27532.1068-0.07730.219-0.1926-0.19740.0311-0.2139-0.00710.0890.0462-0.0797-0.01040.0038-0.1239-0.0124-0.1332113.060820.848749.8821
44.4671-1.78-0.05550.75220.15490.4111-0.01780.3646-0.3811-0.13680.00120.25810.0566-0.06440.0166-0.05410.0331-0.01820.0041-0.01970.049872.055119.036954.835
53.6165-0.7627-0.51881.3258-0.05630.9340.0154-0.1959-0.05980.1707-0.04830.06910.02440.10010.0329-0.1533-0.0035-0.0145-0.1009-0.0046-0.149950.411543.842171.7443
64.0273-1.79130.10990.7976-0.05140.0103-0.1503-0.2388-0.38690.12510.13870.10120.0471-0.01020.0116-0.07230.0380.0315-0.02150.04610.070980.920215.621367.928
74.1650.49430.00262.0981-0.11051.96830.009-0.38130.28410.2741-0.0508-0.1215-0.1330.06090.0418-0.0812-0.06090.0048-0.0962-0.0144-0.1609106.223286.351421.9518
83.1862.20730.34081.53690.25240.07130.0355-0.39670.38770.1233-0.11760.3209-0.0436-0.02140.0821-0.0316-0.05640.0449-0.0041-0.03620.070865.954780.47816.8976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 123
2X-RAY DIFFRACTION2A124 - 219
3X-RAY DIFFRACTION3B21 - 123
4X-RAY DIFFRACTION4B124 - 220
5X-RAY DIFFRACTION5C21 - 123
6X-RAY DIFFRACTION6C124 - 220
7X-RAY DIFFRACTION7D21 - 123
8X-RAY DIFFRACTION8D124 - 219

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