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- PDB-4d6w: Crystal Structure of the low pH conformation of Chandipura Virus ... -

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Basic information

Entry
Database: PDB / ID: 4d6w
TitleCrystal Structure of the low pH conformation of Chandipura Virus glycoprotein G ectodomain
ComponentsGLYCOPROTEIN G
KeywordsVIRAL PROTEIN / RHABDOVIRUS / VIRAL ENTRY / MEMBRANE FUSION
Function / homology
Function and homology information


symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
PH-domain like - #130 / Rhabdovirus spike glycoprotein G, lateral domain / Helix Hairpins - #740 / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Helix Hairpins / PH-domain like / Helix non-globular / Special / SH3 type barrels. ...PH-domain like - #130 / Rhabdovirus spike glycoprotein G, lateral domain / Helix Hairpins - #740 / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Helix Hairpins / PH-domain like / Helix non-globular / Special / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesCHANDIPURA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsBaquero, E. / Albertini, A. / Raux, H. / Bressanelli, S. / Gaudin, Y.
CitationJournal: Plos Pathog. / Year: 2015
Title: Structure of the Low Ph Conformation of Chandipura Virus G Reveals Important Features in the Evolution of the Vesiculovirus Glycoprotein.
Authors: Baquero, E. / Albertini, A.A. / Raux, H. / Buonocore, L. / Rose, J.K. / Bressanelli, S. / Gaudin, Y.
History
DepositionNov 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOPROTEIN G
B: GLYCOPROTEIN G
C: GLYCOPROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,6617
Polymers140,4273
Non-polymers1,2344
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-59.1 kcal/mol
Surface area58010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)365.590, 83.500, 60.820
Angle α, β, γ (deg.)90.00, 96.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GLYCOPROTEIN G


Mass: 46808.914 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, RESIDUES 22-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHANDIPURA VIRUS / Production host: VESICULAR STOMATITIS VIRUS / Strain (production host): INDIANA MUDD-SUMMERS / References: UniProt: P13180
#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: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE ECTODOMAIN (419 RESIDUES) CORRESPONDS TO THE RESIDUES 22 TO 440 OF THE PRECURSOR PROTEIN.

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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: 3.01 Å3/Da / Density % sol: 59.18 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: CRYSTALS WERE OBTAINED AT 293 K BY THE HANGING DROP VAPOUR DIFFUSION METHOD. DROPS WERE PREPARED BY MIXING 1 MICROLITER OF CHAV-GTH (4 MG/ML) SUPPLEMENTED WITH 0.2% N-DODECYL B-MALTOSIDE ...Details: CRYSTALS WERE OBTAINED AT 293 K BY THE HANGING DROP VAPOUR DIFFUSION METHOD. DROPS WERE PREPARED BY MIXING 1 MICROLITER OF CHAV-GTH (4 MG/ML) SUPPLEMENTED WITH 0.2% N-DODECYL B-MALTOSIDE WITH 1 MICROLITER OF THE RESERVOIR SOLUTION (12% PEG 3350, 0.1 M SODIUM ACETATE PH 4.6) AND EQUILIBRATED AGAINST 500 MICROLITERS OF RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.16718
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2012
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.16718 Å / Relative weight: 1
ReflectionResolution: 3.6→49.13 Å / Num. obs: 21199 / % possible obs: 99.3 % / Observed criterion σ(I): 1.79 / Redundancy: 3.1 % / Biso Wilson estimate: 86.05 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.49
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.79 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CMZ

2cmz
PDB Unreleased entry


Resolution: 3.6→49.128 Å / SU ML: 0.5 / σ(F): 2 / Phase error: 27.68 / Stereochemistry target values: ML
Details: RESIDUES 26-33 OF CHAIN A AND 27- -33 OF CHAIN C ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2595 1056 5 %
Rwork0.1933 --
obs0.1966 21188 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→49.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9661 0 80 4 9745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310048
X-RAY DIFFRACTIONf_angle_d1.57113649
X-RAY DIFFRACTIONf_dihedral_angle_d12.9563638
X-RAY DIFFRACTIONf_chiral_restr0.0691485
X-RAY DIFFRACTIONf_plane_restr0.0091730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.76390.34341300.24212493X-RAY DIFFRACTION100
3.7639-3.96220.33661270.22062512X-RAY DIFFRACTION99
3.9622-4.21030.27951370.19392470X-RAY DIFFRACTION99
4.2103-4.53520.26591260.16252517X-RAY DIFFRACTION100
4.5352-4.99120.22641300.15532514X-RAY DIFFRACTION99
4.9912-5.71250.26611310.16782523X-RAY DIFFRACTION99
5.7125-7.19350.241360.20752518X-RAY DIFFRACTION99
7.1935-49.13240.22651390.20912585X-RAY DIFFRACTION98
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)
10.31620.1139-0.20570.180.01030.0539-0.1701-0.1731-0.22590.0480.13520.02370.02140.069800.70480.1082-0.01510.725-0.03740.6656-56.76096.94619.1062
20.3759-0.1744-0.04630.13220.08080.4229-0.02380.2473-0.1878-0.32660.07680.0408-0.11280.09760.07660.5708-0.00620.03430.5547-0.13920.5217-62.16789.7973-17.6425
30.3618-0.15020.10220.0425-0.09360.20770.0080.01290.1575-0.28960.1124-0.3302-0.26220.1209-0.05640.4191-0.11290.03230.5665-0.11480.6383-41.427823.9043-6.2868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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