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- PDB-1urz: Low pH induced, membrane fusion conformation of the envelope prot... -

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Basic information

Entry
Database: PDB / ID: 1urz
TitleLow pH induced, membrane fusion conformation of the envelope protein of tick-borne encephalitis virus
ComponentsENVELOPE PROTEIN
KeywordsVIRUS/VIRAL PROTEIN / ENVELOPE PROTEIN / MEMBRANE FUSION / VIRUS-VIRAL PROTEIN complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M ...Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesTICK-BORNE ENCEPHALITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBressanelli, S. / Rey, F.A.
CitationJournal: Embo J. / Year: 2004
Title: Structure of a Flavivirus Envelope Glycoprotein in its Low-Ph-Induced Membrane Fusion Conformation.
Authors: Bressanelli, S. / Stiasny, K. / Allison, S.L. / Stura, E.A. / Duquerroy, S. / Lescar, J. / Heinz, F.X. / Rey, F.A.
History
DepositionNov 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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: ENVELOPE PROTEIN
B: ENVELOPE PROTEIN
C: ENVELOPE PROTEIN
D: ENVELOPE PROTEIN
E: ENVELOPE PROTEIN
F: ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)262,7396
Polymers262,7396
Non-polymers00
Water6,666370
1
A: ENVELOPE PROTEIN
B: ENVELOPE PROTEIN
C: ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)131,3693
Polymers131,3693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-54.1 kcal/mol
Surface area57750 Å2
MethodPQS
2
D: ENVELOPE PROTEIN
E: ENVELOPE PROTEIN
F: ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)131,3693
Polymers131,3693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-69.6 kcal/mol
Surface area57970 Å2
MethodPQS
Unit cell
Length a, b, c (Å)121.500, 142.900, 173.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.57966, 0.80976, 0.09102), (0.22321, -0.26521, 0.938), (0.78369, -0.5234, -0.33448)-20.55118, -43.38176, 102.40139
2given(0.58609, 0.21247, 0.78189), (0.80658, -0.24463, -0.53813), (0.07694, 0.94605, -0.31475)-58.1938, 59.44635, 75.21166
3given(-0.60776, -0.7852, -0.11868), (0.28167, -0.35287, 0.89227), (-0.74249, 0.50886, 0.43563)21.89181, -35.47573, -18.11276
4given(-0.62015, -0.22672, -0.75101), (0.78393, -0.14306, -0.60414), (0.02953, -0.96339, 0.26646)56.11505, 65.45663, 19.39991
5given(-0.99898, -0.04079, -0.01929), (-0.04269, 0.99288, 0.11121), (0.01461, 0.11192, -0.99361)1.66674, -4.39186, 88.7182
DetailsTHE VIRUS PARTICLE HAS A PROTEIN SHELL WITH ICOSAHEDRAL SYMMETRY MADE OF 180 DIMERS BEFORE EXPOSURE TO LOW PH. AFTER REARRANGEMENT AT LOW PH, THE SHELL LOSES ICOSAHEDRAL SYMMETRY AS THE ENVELOPE REARRANGES INTO 120 TRIMERS.

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Components

#1: Protein
ENVELOPE PROTEIN


Mass: 43789.758 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) TICK-BORNE ENCEPHALITIS VIRUS / Strain: NEUDOERFL / References: UniProt: Q80E47
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57 %
Description: DATA CORRECTED FOR SPINDLE-SHUTTER DESYNCHRONISATION
Crystal growpH: 4.5
Details: PEG 4000 25%, SODIUM ACETATE 0.1M PH 4.5, N,N-DIMETHYLDECYLAMINE N-OXIDE (DDAO) 15 MM
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Stiasny, K., (2004) J. Virol., 78, 3178.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12-5 mg/mlprotein1drop
20.1 Msodium acetate1reservoirpH4.5
320-30 %PEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.34106
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34106 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 80896 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2 / % possible all: 83.9
Reflection
*PLUS
Num. measured all: 306381
Reflection shell
*PLUS
% possible obs: 83.9 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SVB

1svb


Resolution: 2.7→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4090 5.1 %RANDOM
Rwork0.207 ---
obs0.207 80896 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.1336 Å2 / ksol: 0.318351 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.77 Å20 Å20 Å2
2--0.49 Å20 Å2
3---4.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17616 0 0 370 17986
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.161.5
X-RAY DIFFRACTIONc_mcangle_it5.012
X-RAY DIFFRACTIONc_scbond_it5.172
X-RAY DIFFRACTIONc_scangle_it7.432.5
Refine LS restraints NCSRms dev Biso : 4.11 Å2 / Rms dev position: 0.36 Å / Weight Biso : 2 / Weight position: 10
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 598 5.1 %
Rwork0.305 11019 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.316

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