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- PDB-2wfo: Crystal structure of Machupo virus envelope glycoprotein GP1 -

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Basic information

Entry
Database: PDB / ID: 2wfo
TitleCrystal structure of Machupo virus envelope glycoprotein GP1
ComponentsGLYCOPROTEIN 1
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / ARENAVIRUS / NEW WORLD ARENAVIRUS / HEMORRHAGIC FEVER VIRUS / ENVELOPE PROTEIN / MACHUPO / JUNIN / GUANARITO / SABIA / CHAPARE / VIRION / MACV / GP1 / VIRAL ATTACHMENT / TRANSFERRIN RECEPTOR
Function / homologyArenavirus glycoprotein / Arenavirus glycoprotein / viral envelope / membrane / Glycoprotein 1
Function and homology information
Biological speciesMachupo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.73 Å
AuthorsBowden, T.A. / Crispin, M. / Graham, S.C. / Harvey, D.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I.
CitationJournal: J.Virol. / Year: 2009
Title: Unusual Molecular Architecture of the Machupo Virus Attachment Glycoprotein.
Authors: Bowden, T.A. / Crispin, M. / Graham, S.C. / Harvey, D.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I.
History
DepositionApr 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOPROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1395
Polymers21,0511
Non-polymers1,0884
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.523, 55.070, 61.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLYCOPROTEIN 1 / MACV-GP1


Mass: 21050.939 Da / Num. of mol.: 1 / Fragment: TFR1 RECEPTOR BINDING DOMAIN, RESIDUES 87-257
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE ASN95, ASN137, ASN166, AND ASN178
Source: (gene. exp.) Machupo virus / Description: SYNTHETICALLY OPTIMIZED CDNA (CODON DEVICES) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6PXS3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.5 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growpH: 5.5
Details: 25% (W/V) PEG 3350, 0.2 M NACL, AND 0.1 M BIS-TRIS (PH 5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Details: VERTICALLY BENDED MULTILAYER
RadiationMonochromator: DIAMOND (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 18458 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.5 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.73→32.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.738 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES CONTAIN TLS CONTRIBUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 943 5.1 %RANDOM
Rwork0.172 ---
obs0.174 17465 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.67 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 70 198 1498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221350
X-RAY DIFFRACTIONr_bond_other_d0.0010.02921
X-RAY DIFFRACTIONr_angle_refined_deg1.382.0081828
X-RAY DIFFRACTIONr_angle_other_deg0.8732221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85724.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15715223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.166156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.761.5765
X-RAY DIFFRACTIONr_mcbond_other0.1841.5312
X-RAY DIFFRACTIONr_mcangle_it1.46721232
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2113585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5584.5596
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: 1.73→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 69 -
Rwork0.23 1163 -
obs--90.12 %
Refinement TLS params.Method: refined / Origin x: 33.003 Å / Origin y: 36.283 Å / Origin z: 5.022 Å
111213212223313233
T0.0045 Å2-0.0032 Å2-0.0051 Å2-0.0305 Å2-0.0063 Å2--0.017 Å2
L0.7093 °2-0.0912 °2-0.1682 °2-0.6423 °2-0.038 °2--0.5581 °2
S-0.0016 Å °-0.0356 Å °0.017 Å °0.0081 Å °-0.0024 Å °-0.0268 Å °0.0265 Å °0.0187 Å °0.004 Å °

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