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- PDB-4g2k: Crystal structure of the Marburg Virus GP2 ectodomain in its post... -

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Basic information

Entry
Database: PDB / ID: 4g2k
TitleCrystal structure of the Marburg Virus GP2 ectodomain in its post-fusion conformation
ComponentsGeneral control protein GCN4, Envelope glycoprotein GP2 chimera
KeywordsVIRAL PROTEIN / gp2-gcn4 fusion
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / membrane => GO:0016020 / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / virion attachment to host cell / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
TLV/ENV coat polyprotein / Helix Hairpins - #210 / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily ...TLV/ENV coat polyprotein / Helix Hairpins - #210 / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Envelope glycoprotein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Lake Victoria marburgvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Koellhoffer, J.F. / Harrison, J.S. / Toro, R. / Bhosle, R.C. / Chandran, K. / Lai, J.R. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal Structure of the Marburg Virus GP2 Core Domain in Its Postfusion Conformation.
Authors: Koellhoffer, J.F. / Malashkevich, V.N. / Harrison, J.S. / Toro, R. / Bhosle, R.C. / Chandran, K. / Almo, S.C. / Lai, J.R.
History
DepositionJul 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General control protein GCN4, Envelope glycoprotein GP2 chimera
B: General control protein GCN4, Envelope glycoprotein GP2 chimera
C: General control protein GCN4, Envelope glycoprotein GP2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2956
Polymers44,0763
Non-polymers2203
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-127 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.574, 147.529, 42.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-828-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
111
121
131
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein General control protein GCN4, Envelope glycoprotein GP2 chimera / Amino acid biosynthesis regulatory protein / virion spike glycoprotein


Mass: 14691.900 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Lake Victoria marburgvirus
Gene: GCN4, GP, GP2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03069, UniProt: P35254
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN IS A CHIMERA COMPRISING AN N-TERMINAL EXPRESSION TAG, THE LEUCINE ZIPPER DOMAIN (UNP ...THE PROTEIN IS A CHIMERA COMPRISING AN N-TERMINAL EXPRESSION TAG, THE LEUCINE ZIPPER DOMAIN (UNP RESIDUES 250-279) OF GCN4, AND THE ECTODOMAIN (UNP RESIDUES 554-633) OF GP2.

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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: 1.86 Å3/Da / Density % sol: 33.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M sodium acetate, 0.085 M Tris-HCl, pH 8.5, 25.5% PEG3350, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26888 / % possible obs: 99.6 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.071 / Χ2: 1.074 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.935.90.77512660.987194.3
1.93-1.976.70.60412860.98198.8
1.97-2.0180.53913340.973199.8
2.01-2.0510.10.51213181.019199.9
2.05-2.0910.50.36813121.0171100
2.09-2.1410.50.31513321.0461100
2.14-2.1910.50.26113471.0381100
2.19-2.2510.50.20313201.0731100
2.25-2.3210.50.18113241.0681100
2.32-2.3910.40.15613361.0941100
2.39-2.4810.40.13313361.1581100
2.48-2.5810.30.11413191.1751100
2.58-2.710.30.09613601.1391100
2.7-2.8410.40.08113551.1741100
2.84-3.0210.20.06513451.0861100
3.02-3.2510.10.06213611.1191100
3.25-3.589.90.05313651.1671100
3.58-4.099.70.04913670.979199.9
4.09-5.169.80.04314091.111100
5.16-5090.03614960.967199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.52 Å
Translation2.5 Å49.52 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 26836
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.42-10035.20.56513
5.86-7.4249.30.597501
5.09-5.8650.50.615516
4.56-5.0941.60.611563
4.17-4.5640.90.701614
3.86-4.1738.40.709669
3.61-3.8645.50.639725
3.41-3.6149.20.609754
3.23-3.4148.20.628793
3.08-3.2354.70.594830
2.95-3.0850.90.579871
2.84-2.9549.50.599900
2.74-2.8452.60.597956
2.64-2.7453.20.619958
2.56-2.6457.80.5571012
2.48-2.5654.70.613997
2.41-2.4856.80.5251082
2.35-2.4155.50.5491088
2.29-2.3559.30.5751106
2.23-2.2959.30.5751144
2.18-2.2359.10.5391165
2.14-2.1859.40.5261195
2.09-2.1463.10.4961221
2.05-2.0961.10.5171240
2.01-2.0564.40.4651264
1.97-2.0166.90.5141297
1.94-1.9768.40.4751283
1.89-1.9472.90.4921579

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
DM6.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EBO

2ebo


Resolution: 1.9→19.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2426 / WRfactor Rwork: 0.1908 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8227 / SU B: 7.38 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1777 / SU Rfree: 0.1629 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1336 5 %RANDOM
Rwork0.1956 ---
obs0.198 26608 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.37 Å2 / Biso mean: 35.2613 Å2 / Biso min: 18.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 13 251 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192725
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.983665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.175338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17124.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39115579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0111527
X-RAY DIFFRACTIONr_chiral_restr0.0850.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021949
Refine LS restraints NCS
Ens-IDDom-IDNumberRefine-IDTypeRms dev position (Å)Weight position
11168X-RAY DIFFRACTIONTIGHT THERMAL4.0914.14
21166X-RAY DIFFRACTIONTIGHT THERMAL4.2914.14
31164X-RAY DIFFRACTIONTIGHT THERMAL3.4714.14
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 97 -
Rwork0.255 1763 -
all-1860 -
obs--96.27 %
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)
10.2462-0.13710.09542.3881-2.39222.756-0.0372-0.0175-0.00770.1012-0.0434-0.0604-0.08320.03390.08060.0226-0.01180.00520.07210.01340.047814.4891-27.46975.4627
20.13220.196-0.27750.9817-1.20711.955-0.07270.0131-0.0527-0.12590.11570.02610.1761-0.1467-0.0430.0458-0.020.00760.0770.02690.099513.8891-31.89291.8409
30.12540.2094-0.422.5747-2.43082.8547-0.0415-0.0129-0.04-0.092-0.0584-0.07570.1250.09160.09990.037-0.0145-0.01980.10480.03070.137519.2152-29.842.738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A524 - 633
2X-RAY DIFFRACTION1A701
3X-RAY DIFFRACTION2B524 - 631
4X-RAY DIFFRACTION3C525 - 631
5X-RAY DIFFRACTION3C700

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