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- PDB-5nsj: GP1 receptor-binding domain from Whitewater Arroyo mammarenavirus -

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Basic information

Entry
Database: PDB / ID: 5nsj
TitleGP1 receptor-binding domain from Whitewater Arroyo mammarenavirus
ComponentsPre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Viral glycoprotein / receptor binding domain
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 / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
SAMARIUM (III) ION / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesWhitewater Arroyo mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsShimon, A. / Shani, O. / Diskin, R.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation682/16 Israel
I-CORE1775/12 Israel
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Basis for Receptor Selectivity by the Whitewater Arroyo Mammarenavirus.
Authors: Shimon, A. / Shani, O. / Diskin, R.
History
DepositionApr 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Refinement description / Structure summary
Category: citation / software / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _software.classification / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_struct_conn_angle / pdbx_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
B: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,27213
Polymers37,5622
Non-polymers2,70911
Water6,035335
1
A: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2317
Polymers18,7811
Non-polymers1,4506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0406
Polymers18,7811
Non-polymers1,2595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.024, 128.352, 45.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

21A-466-

HOH

31A-508-

HOH

41A-512-

HOH

51A-548-

HOH

61B-450-

HOH

71B-577-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pre-glycoprotein polyprotein GP complex


Mass: 18781.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Whitewater Arroyo mammarenavirus / Strain: isolate Rat/United States/AV 9310135/1995 / Gene: GPC, GP-C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q911P0

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Sugars , 3 types, 4 molecules

#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.: 2
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-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 1
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

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Non-polymers , 2 types, 342 molecules

#4: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Sm
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris HCL pH 8.7, 0.2 M ammonium acetate, 33% w/v polyethylene glycol 3,350, 5% ethylene glycol, 3% 1,1,1,3,3,3-hexafluro-2-propanol, 50 mM sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.377 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.377 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. obs: 35366 / % possible obs: 98.7 % / Redundancy: 6 % / CC1/2: 0.997 / Net I/σ(I): 7.9
Reflection shellResolution: 2.249→2.31 Å / Rmerge(I) obs: 0.969 / CC1/2: 0.739 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMACis phenix, but edited to fix R-factor: ACrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAS

3kas


Resolution: 2.249→45.321 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.17
RfactorNum. reflection% reflection
Rfree0.2091 1605 5.41 %
Rwork0.1828 --
obs0.1862 29679 85.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.249→45.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 116 335 2705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082433
X-RAY DIFFRACTIONf_angle_d1.1383324
X-RAY DIFFRACTIONf_dihedral_angle_d8.6761434
X-RAY DIFFRACTIONf_chiral_restr0.065394
X-RAY DIFFRACTIONf_plane_restr0.008417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2534-2.3260.3196810.25291431X-RAY DIFFRACTION46
2.326-2.4090.27341360.24181716X-RAY DIFFRACTION55
2.409-2.50520.26251350.23491967X-RAY DIFFRACTION63
2.5052-2.61890.26111270.23552337X-RAY DIFFRACTION74
2.6189-2.75660.26241420.21852709X-RAY DIFFRACTION87
2.7566-2.92870.23941460.21942980X-RAY DIFFRACTION94
2.9287-3.15380.23411620.20082958X-RAY DIFFRACTION95
3.1538-3.46940.19131540.17252982X-RAY DIFFRACTION95
3.4694-3.96720.18411850.16012941X-RAY DIFFRACTION94
3.9672-4.98250.16121340.13943012X-RAY DIFFRACTION96
4.9825-18.66910.19411540.17642996X-RAY DIFFRACTION95
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)
18.21772.48967.23628.61681.18976.4998-0.36031.1376-0.0548-0.33950.4863-0.94050.14430.4149-0.16420.3997-0.00450.01770.20930.04450.2366-10.4905-8.0516-16.383
26.346-0.2698-2.4323.41680.04283.0034-0.11980.6410.1352-0.52650.1203-0.36630.1056-0.1333-0.01250.2073-0.001-0.00130.11720.02470.1773-16.6512-14.9252-14.0292
34.0901-2.667-2.3936.14271.22351.42590.2443-0.7427-0.71160.39120.0587-0.09460.47770.6629-0.08960.1630.0003-0.03350.3964-0.00110.5907-25.0308-25.60292.6006
41.7582-2.2858-1.34576.8842.28622.61610.44430.30020.2359-0.21510.0277-1.0091-0.05880.2537-0.11840.68170.2417-0.0650.3298-0.04540.3333-14.0623-18.98523.9738
50.21130.2739-0.02030.3554-0.03240.1397-0.0460.34150.1903-0.10050.16740.37740.1242-0.3126-0.07220.4135-0.0664-0.21690.841-0.23111.1761-5.1404-25.4822-7.6913
64.104-3.76650.73179.21963.72723.4873-0.4266-0.37190.22530.8445-0.18460.28230.2974-0.16740.5620.3463-0.00260.01140.17990.0530.5068-8.4348-12.5325-5.2289
72.71950.2367-0.65032.52823.76845.9856-0.03380.1060.41120.12320.2868-0.43810.140.1916-0.21310.1467-0.0001-0.08050.16320.03010.2246-20.357-16.54252.0492
81.8984-2.3937-0.98393.0211.146.129-0.459-0.13420.09960.22550.0662-0.0603-0.1645-0.16650.10090.2343-0.0501-0.04360.1111-0.08490.2458-23.5279-4.453-3.9276
96.98971.5273-2.4422.77822.05933.6035-0.010.2670.3301-0.0974-0.14750.5133-0.0797-0.45140.11780.18130.0161-0.06460.09810.00840.3408-31.8497-8.418-7.1164
104.23150.2875-4.24635.22331.92535.2019-0.03791.09550.2853-1.50620.5902-0.556-0.677-0.6533-0.46160.5403-0.05330.06390.403-0.04590.2577-17.3699-18.0228-14.7748
115.16991.21070.18541.32960.3933.3654-0.24991.04090.1975-0.37730.2390.07910.15460.2730.13260.21420.0117-0.01090.3196-0.04490.1993-50.986-15.2735-3.1343
124.77730.3963-1.53723.1853-2.66495.39080.0923-0.16170.22470.64930.0639-0.1036-0.19740.8812-0.07230.25650.0381-0.0750.2836-0.09590.3688-41.1815-16.431112.1859
133.63221.613-0.07675.4895-0.45110.92480.08910.073-0.2197-0.0738-0.06520.01170.0175-0.0359-0.04220.1879-0.0087-0.02340.1226-0.00410.1956-51.4519-20.54427.3007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 79 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 148 )
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 194 )
9X-RAY DIFFRACTION9chain 'A' and (resid 195 through 207 )
10X-RAY DIFFRACTION10chain 'A' and (resid 208 through 220 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 137 )
13X-RAY DIFFRACTION13chain 'B' and (resid 138 through 220 )

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