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- PDB-3phf: Crystal Structure of the Epstein-Barr virus gH and gL complex -

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Basic information

Entry
Database: PDB / ID: 3phf
TitleCrystal Structure of the Epstein-Barr virus gH and gL complex
Components
  • Envelope glycoprotein H
  • Envelope glycoprotein L
KeywordsVIRAL PROTEIN / VIRUS ENTRY / MEMBRANE FUSION / GLYCOPROTEIN
Function / homology
Function and homology information


host cell endosome membrane / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal ...Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.58 Å
AuthorsMatsuura, H. / Kirschner, A.N. / Jardetzky, T.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of the Epstein-Barr virus (EBV) glycoprotein H/glycoprotein L (gH/gL) complex.
Authors: Matsuura, H. / Kirschner, A.N. / Longnecker, R. / Jardetzky, T.S.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Envelope glycoprotein H
D: Envelope glycoprotein L
E: Envelope glycoprotein H
F: Envelope glycoprotein L
G: Envelope glycoprotein H
H: Envelope glycoprotein L
I: Envelope glycoprotein H
J: Envelope glycoprotein L
K: Envelope glycoprotein H
L: Envelope glycoprotein L
M: Envelope glycoprotein H
N: Envelope glycoprotein L
O: Envelope glycoprotein H
P: Envelope glycoprotein L
Q: Envelope glycoprotein H
R: Envelope glycoprotein L
S: Envelope glycoprotein H
T: Envelope glycoprotein L
U: Envelope glycoprotein H
V: Envelope glycoprotein L
W: Envelope glycoprotein H
X: Envelope glycoprotein L
Y: Envelope glycoprotein H
Z: Envelope glycoprotein L
1: Envelope glycoprotein H
2: Envelope glycoprotein L
3: Envelope glycoprotein H
4: Envelope glycoprotein L
5: Envelope glycoprotein H
6: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)1,347,94432
Polymers1,347,94432
Non-polymers00
Water00
1
A: Envelope glycoprotein H
B: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Envelope glycoprotein H
D: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Envelope glycoprotein H
F: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Envelope glycoprotein H
H: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Envelope glycoprotein H
J: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Envelope glycoprotein H
L: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Envelope glycoprotein H
N: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Envelope glycoprotein H
P: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Envelope glycoprotein H
R: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: Envelope glycoprotein H
T: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Envelope glycoprotein H
V: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Envelope glycoprotein H
X: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
Y: Envelope glycoprotein H
Z: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
1: Envelope glycoprotein H
2: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
3: Envelope glycoprotein H
4: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
5: Envelope glycoprotein H
6: Envelope glycoprotein L


Theoretical massNumber of molelcules
Total (without water)84,2472
Polymers84,2472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.510, 244.909, 287.950
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Envelope glycoprotein H / gH / Glycoprotein 85 / gp85


Mass: 72324.016 Da / Num. of mol.: 16 / Fragment: EXTRACELLULAR DOMAIN (unp residue 20-672)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BXLF2, gH / Plasmid: pBACgus4x-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03231
#2: Protein
Envelope glycoprotein L / gL / Glycoprotein 25 / gp25


Mass: 11922.500 Da / Num. of mol.: 16 / Fragment: EXTRACELLULAR DOMAIN (unp residues 24-131)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BKRF2, GL / Plasmid: pBACgus4x-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03212

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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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2008
RadiationMonochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.5→28.868 Å / Num. all: 261791 / Num. obs: 261791 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.5-3.69197.4
3.69-3.91199.1
3.91-4.18199.9
4.18-4.521100
4.52-4.951100
4.95-5.531100
5.53-6.391100
6.39-7.831100
7.83-11.071100
11.07-28.868194.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.58→28.868 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3128 2461 -RANDOM
Rwork0.2838 ---
all-245994 --
obs-245098 99.6 %-
Refinement stepCycle: LAST / Resolution: 3.58→28.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94656 0 0 0 94656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003209
X-RAY DIFFRACTIONc_angle_deg0.88433
X-RAY DIFFRACTIONc_mcbond_it13.258
X-RAY DIFFRACTIONc_scbond_it21.027
X-RAY DIFFRACTIONc_mcangle_it18.047
X-RAY DIFFRACTIONc_scangle_it24.671

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