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- PDB-3mko: Crystal Structure of the Lymphocytic Choriomeningitis Virus Membr... -

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Basic information

Entry
Database: PDB / ID: 3mko
TitleCrystal Structure of the Lymphocytic Choriomeningitis Virus Membrane Fusion Glycoprotein GP2 in its Postfusion Conformation
ComponentsGlycoprotein C
KeywordsVIRAL PROTEIN / Trimeric coiled-coil
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Helix Hairpins - #1590 / Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
URANYL (VI) ION / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsIgonet, S. / Vaney, M.C. / Rey, F.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: X-ray structure of the arenavirus glycoprotein GP2 in its postfusion hairpin conformation
Authors: Igonet, S. / Vaney, M.C. / Vonhrein, C. / Bricogne, G. / Stura, E.A. / Hengartner, H. / Eschli, B. / Rey, F.A.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Dec 28, 2011Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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: Glycoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7816
Polymers16,1211
Non-polymers6605
Water1,63991
1
A: Glycoprotein C
hetero molecules

A: Glycoprotein C
hetero molecules

A: Glycoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,34418
Polymers48,3643
Non-polymers1,98015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10830 Å2
ΔGint-118 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.925, 52.925, 191.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-95-

CL

21A-96-

IUM

31A-68-

HOH

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Components

#1: Protein Glycoprotein C / Arenavirus Glycoprotein 2


Mass: 16121.222 Da / Num. of mol.: 1 / Fragment: Ectodomain / Mutation: C316S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis virus / Strain: WE-HPI / Gene: lcmv-GP / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3) / References: UniProt: Q9ICW1
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2U
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHESE FOUR RESIDUES CORRESPOND TO A PROTEASE (FACTOR XA) CLEAVAGE SITE

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% MPD, 2% PEG 400, 100mM imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3354 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2008 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3354 Å / Relative weight: 1
ReflectionResolution: 1.8→37.22 Å / Num. obs: 13777 / % possible obs: 89.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 26.9
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1911 / Rsym value: 0.463 / % possible all: 88.2

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Processing

Software
NameVersionClassification
MAR345data collection
SHARPphasing
BUSTER-TNT2.7.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→37.22 Å / Cor.coef. Fo:Fc: 0.9454 / Cor.coef. Fo:Fc free: 0.9283 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.112
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=LG1 NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=37. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=LG1 NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=37. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 694 5.04 %RANDOM
Rwork0.1883 ---
all0.19 ---
obs-13771 87.91 %-
Displacement parametersBiso mean: 27.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.2928 Å20 Å20 Å2
2---0.2928 Å20 Å2
3---0.5856 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.125 Å0.186 Å
Luzzati sigma a0.12 Å-
Refinement stepCycle: LAST / Resolution: 1.8→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms854 0 28 91 973
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01929HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.991259HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d328SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes129HARMONIC5
X-RAY DIFFRACTIONt_it929HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion17.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion117SEMIHARMONIC5
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_contact1197SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.94 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.216 158 5.71 %
Rwork0.194 2608 -
all0.1953 2766 -
obs--87.91 %

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