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- PDB-6p72: Crystal Structure of the Cedar henipavirus Attachment G Glycoprot... -

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Basic information

Entry
Database: PDB / ID: 6p72
TitleCrystal Structure of the Cedar henipavirus Attachment G Glycoprotein global domain
ComponentsAttachment glycoprotein
KeywordsVIRAL PROTEIN / Cedar virus / attachment / glycoprotein
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Attachment glycoprotein
Similarity search - Component
Biological speciesCedar virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.283 Å
AuthorsXu, K. / Nikolov, D.B. / Xu, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural and functional analyses reveal promiscuous and species specific use of ephrin receptors by Cedar virus.
Authors: Laing, E.D. / Navaratnarajah, C.K. / Cheliout Da Silva, S. / Petzing, S.R. / Xu, Y. / Sterling, S.L. / Marsh, G.A. / Wang, L.F. / Amaya, M. / Nikolov, D.B. / Cattaneo, R. / Broder, C.C. / Xu, K.
History
DepositionJun 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / database_PDB_caveat / 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_validate_chiral / 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 / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment glycoprotein
C: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,64716
Polymers97,9102
Non-polymers5,73614
Water00
1
A: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7419
Polymers48,9551
Non-polymers2,7868
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9067
Polymers48,9551
Non-polymers2,9516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.675, 211.675, 113.194
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA197 - 5622
211chain CC197 - 5625

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Components

#1: Protein Attachment glycoprotein


Mass: 48955.164 Da / Num. of mol.: 2 / Fragment: global domain (UNP residues 194-622)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cedar virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: J7H333
#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.: 7
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-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 7.48 Å3/Da / Density % sol: 83.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES, pH 6.0, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 43933 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 108.87 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.047 / Rrim(I) all: 0.105 / Χ2: 1.065 / Net I/σ(I): 6.8 / Num. measured all: 320698
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.3-3.426.943530.5740.5620.74799.7
3.42-3.55743450.7130.4010.76299.70.992
3.55-3.72743880.8890.2390.79299.80.5920.639
3.72-3.917.243440.9370.160.79399.80.40.431
3.91-4.167.443990.9730.10.83499.80.2550.274
4.16-4.487.643630.990.0590.95899.90.1530.164
4.48-4.937.644230.9950.0371.1581000.0960.103
4.93-5.647.643680.9960.0331.2411000.0850.091
5.64-7.17.544470.9970.0291.3731000.0740.079
7.1-507.245030.9980.0181.90499.90.0450.048

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.283→45.829 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2315 1993 4.55 %
Rwork0.2061 --
obs0.2073 43830 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 197.9 Å2 / Biso mean: 62.17 Å2 / Biso min: 18.2 Å2
Refinement stepCycle: final / Resolution: 3.283→45.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6820 0 377 0 7197
Biso mean--98.72 --
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017413
X-RAY DIFFRACTIONf_angle_d1.42110074
X-RAY DIFFRACTIONf_chiral_restr0.061162
X-RAY DIFFRACTIONf_plane_restr0.0081245
X-RAY DIFFRACTIONf_dihedral_angle_d22.9452762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3827X-RAY DIFFRACTION14.721TORSIONAL
12C3827X-RAY DIFFRACTION14.721TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2826-3.36460.36731300.32062703283390
3.3646-3.45560.29771410.292129723113100
3.4556-3.55720.29961440.261629773121100
3.5572-3.6720.27761390.242930203159100
3.672-3.80320.27451460.221229883134100
3.8032-3.95540.24191360.202930153151100
3.9554-4.13530.2261460.192230243170100
4.1353-4.35310.18821460.176429973143100
4.3531-4.62560.18061440.152830203164100
4.6256-4.98240.18071400.145929913131100
4.9824-5.48310.19771400.172830383178100
5.4831-6.27470.2451490.192330213170100
6.2747-7.89890.26431420.225430473189100
7.8989-45.83340.23331500.24073024317497
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)
10.0895-0.0560.03110.0554-0.02010.02230.01150.1063-0.1065-0.1091-0.08220.1710.04570.0381-0.02890.4684-0.192-0.01740.2412-0.13450.154-96.861319.2364-1.6903
20.13860.02480.06030.06130.00270.1386-0.0171-0.07010.2242-0.0290.1210.0063-0.21240.29350.1540.6384-0.1753-0.08490.0143-0.05060.2405-91.568733.110716.9906
30.0633-0.0114-0.01490.14310.12790.1050.0486-0.04350.1683-0.04860.1611-0.0457-0.1290.13590.41580.4497-0.3494-0.14750.0562-0.06050.1304-89.446139.45255.1928
4-0.00250.0106-0.00470.0347-0.01030.0089-0.03190.02670.0347-0.12710.03250.04410.0086-0.0427-0.00220.6762-0.3187-0.08480.1426-0.0560.2173-101.99326.271-1.7079
50.13660.07380.11650.04240.00860.3415-0.02290.0467-0.0845-0.01530.1160.12440.07660.17960.00770.73310.07330.06460.196-0.00010.534-93.0038-31.9638-10.2984
60.0545-0.02540.00150.0411-0.01720.03540.0475-0.0206-0.0679-0.1166-0.00820.0440.12070.04450.10.65410.25090.01150.14790.06580.1637-92.6254-31.27874.5867
70.127-0.0671-0.04880.08090.06110.08620.0797-0.07520.25230.2334-0.01090.1505-0.2055-0.01570.13011.04140.4840.17550.3357-0.13490.4209-96.1207-10.31549.5134
80.15490.10790.02420.1770.01440.14110.0878-0.01870.09220.08790.13850.1556-0.13110.01210.35130.54380.1414-0.05990.0805-0.19560.4428-96.6171-9.2685-2.2716
90.01710.00020.00550.04340.02530.0652-0.11970.05690.0209-0.01350.02770.18390.11030.0198-0.07870.65410.06750.2186-0.0445-0.00360.4517-101.0926-25.6115-9.8493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 197 through 237 )A197 - 237
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 428 )A238 - 428
3X-RAY DIFFRACTION3chain 'A' and (resid 429 through 547 )A429 - 547
4X-RAY DIFFRACTION4chain 'A' and (resid 548 through 622 )A548 - 622
5X-RAY DIFFRACTION5chain 'C' and (resid 197 through 237 )C197 - 237
6X-RAY DIFFRACTION6chain 'C' and (resid 238 through 295 )C238 - 295
7X-RAY DIFFRACTION7chain 'C' and (resid 296 through 428 )C296 - 428
8X-RAY DIFFRACTION8chain 'C' and (resid 429 through 520 )C429 - 520
9X-RAY DIFFRACTION9chain 'C' and (resid 521 through 622 )C521 - 622

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