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- PDB-3d11: Crystal Structures of the Nipah G Attachment Glycoprotein -

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Basic information

Entry
Database: PDB / ID: 3d11
TitleCrystal Structures of the Nipah G Attachment Glycoprotein
ComponentsHemagglutinin-neuraminidase
KeywordsHYDROLASE / beta propeller / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Signal-anchor / Transmembrane / Virion
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Glycoprotein G
Similarity search - Component
Biological speciesNipah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.306 Å
AuthorsXu, K. / Rajashankar, K.R. / Chan, Y.P. / Himanen, P. / Broder, C.C. / Nikolov, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3.
Authors: Xu, K. / Rajashankar, K.R. / Chan, Y.P. / Himanen, J.P. / Broder, C.C. / Nikolov, D.B.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / 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_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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.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 / _struct_ref_seq_dif.details
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: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,35924
Polymers47,9671
Non-polymers4,39223
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.161, 130.161, 130.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-4-

IOD

21A-1460-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemagglutinin-neuraminidase /


Mass: 47966.520 Da / Num. of mol.: 1 / Fragment: UNP residues 176-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Gene: HN / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q9IH62, exo-alpha-sialidase

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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 beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-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
DManpb1-3[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]/1-1-2-2-3/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)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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, 229 molecules

#5: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 3350, KI, pH 6.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.5498 Å
DetectorDate: Aug 18, 2007
RadiationMonochromator: S / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 55607 / % possible obs: 88.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.381.40.357142.6
2.38-2.481.90.318166.8
2.48-2.592.60.293182.9
2.59-2.733.40.257194.6
2.73-2.93.70.185199.2
2.9-3.123.70.127199.6
3.12-3.443.70.096199.9
3.44-3.933.70.0831100
3.93-4.953.60.0771100
4.95-403.70.06199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementResolution: 2.306→39.245 Å / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.257 2519 4.76 %
Rwork0.228 --
obs-52865 84.2 %
Solvent computationBsol: 38.278 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 42.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.306→39.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 150 210 3721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.757
X-RAY DIFFRACTIONf_dihedral_angle_d16.421
X-RAY DIFFRACTIONf_chiral_restr0.056
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.306-2.3140.324132X-RAY DIFFRACTION10121
2.314-2.3220.336176X-RAY DIFFRACTION10127
2.322-2.330.34166X-RAY DIFFRACTION10125
2.33-2.3380.288194X-RAY DIFFRACTION10135
2.338-2.3460.273200X-RAY DIFFRACTION10132
2.346-2.3540.338237X-RAY DIFFRACTION10136
2.354-2.3620.308238X-RAY DIFFRACTION10139
2.362-2.3710.309241X-RAY DIFFRACTION10142
2.371-2.3790.296309X-RAY DIFFRACTION10145
2.379-2.3880.306284X-RAY DIFFRACTION10151
2.388-2.3970.289329X-RAY DIFFRACTION10150
2.397-2.4060.307294X-RAY DIFFRACTION10149
2.406-2.4150.262344X-RAY DIFFRACTION10152
2.415-2.4240.317338X-RAY DIFFRACTION10155
2.424-2.4330.313315X-RAY DIFFRACTION10155
2.433-2.4430.307350X-RAY DIFFRACTION10155
2.443-2.4530.273432X-RAY DIFFRACTION10162
2.453-2.4620.301322X-RAY DIFFRACTION10159
2.462-2.4720.271383X-RAY DIFFRACTION10161
2.472-2.4820.298412X-RAY DIFFRACTION10165
2.482-2.4930.275393X-RAY DIFFRACTION10164
2.493-2.5030.268434X-RAY DIFFRACTION10166
2.503-2.5140.289387X-RAY DIFFRACTION10169
2.514-2.5250.293467X-RAY DIFFRACTION10172
2.525-2.5360.283427X-RAY DIFFRACTION10171
2.536-2.5470.276430X-RAY DIFFRACTION10169
2.547-2.5580.276462X-RAY DIFFRACTION10171
2.558-2.570.271419X-RAY DIFFRACTION10173
2.57-2.5820.273472X-RAY DIFFRACTION10175
2.582-2.5940.312511X-RAY DIFFRACTION10178
2.594-2.6060.274476X-RAY DIFFRACTION10177
2.606-2.6190.288473X-RAY DIFFRACTION10177
2.619-2.6310.278468X-RAY DIFFRACTION10175
2.631-2.6440.281486X-RAY DIFFRACTION10180
2.644-2.6580.286510X-RAY DIFFRACTION10180
2.658-2.6710.272521X-RAY DIFFRACTION10185
2.671-2.6850.281506X-RAY DIFFRACTION10183
2.685-2.6990.265547X-RAY DIFFRACTION10187
2.699-2.7140.274568X-RAY DIFFRACTION10187
2.714-2.7280.248511X-RAY DIFFRACTION10187
2.728-2.7430.286504X-RAY DIFFRACTION10181
2.743-2.7590.292534X-RAY DIFFRACTION10185
2.759-2.7750.244587X-RAY DIFFRACTION10190
2.775-2.7910.267514X-RAY DIFFRACTION10187
2.791-2.8070.267540X-RAY DIFFRACTION10187
2.807-2.8240.264568X-RAY DIFFRACTION10188
2.824-2.8420.271532X-RAY DIFFRACTION10189
2.842-2.8590.257541X-RAY DIFFRACTION10190
2.859-2.8770.232573X-RAY DIFFRACTION10192
2.877-2.8960.27591X-RAY DIFFRACTION10188
2.896-2.9150.273564X-RAY DIFFRACTION10193
2.915-2.9350.253540X-RAY DIFFRACTION10192
2.935-2.9550.229563X-RAY DIFFRACTION10188
2.955-2.9760.234558X-RAY DIFFRACTION10188
2.976-2.9970.256567X-RAY DIFFRACTION10192
2.997-3.0190.235565X-RAY DIFFRACTION10193
3.019-3.0420.261552X-RAY DIFFRACTION10193
3.042-3.0660.266600X-RAY DIFFRACTION10192
3.066-3.090.227565X-RAY DIFFRACTION10194
3.09-3.1150.243551X-RAY DIFFRACTION10192
3.115-3.140.244569X-RAY DIFFRACTION10193
3.14-3.1670.244602X-RAY DIFFRACTION10191
3.167-3.1940.23587X-RAY DIFFRACTION10193
3.194-3.2230.245571X-RAY DIFFRACTION10194
3.223-3.2530.221591X-RAY DIFFRACTION10195
3.253-3.2830.201579X-RAY DIFFRACTION10193
3.283-3.3150.227564X-RAY DIFFRACTION10192
3.315-3.3480.212630X-RAY DIFFRACTION10197
3.348-3.3830.216575X-RAY DIFFRACTION10194
3.383-3.4190.218585X-RAY DIFFRACTION10196
3.419-3.4560.199597X-RAY DIFFRACTION10196
3.456-3.4950.193564X-RAY DIFFRACTION10196
3.495-3.5360.194617X-RAY DIFFRACTION10194
3.536-3.580.189581X-RAY DIFFRACTION10195
3.58-3.6250.207591X-RAY DIFFRACTION10195
3.625-3.6720.191591X-RAY DIFFRACTION10196
3.672-3.7230.193597X-RAY DIFFRACTION10195
3.723-3.7760.186590X-RAY DIFFRACTION10195
3.776-3.8320.19624X-RAY DIFFRACTION10193
3.832-3.8920.193522X-RAY DIFFRACTION10193
3.892-3.9560.196594X-RAY DIFFRACTION10194
3.956-4.0240.196575X-RAY DIFFRACTION10195
4.024-4.0970.169613X-RAY DIFFRACTION10192
4.097-4.1760.165556X-RAY DIFFRACTION10193
4.176-4.2610.177591X-RAY DIFFRACTION10196
4.261-4.3530.162594X-RAY DIFFRACTION10193
4.353-4.4550.153571X-RAY DIFFRACTION10192
4.455-4.5660.161571X-RAY DIFFRACTION10195
4.566-4.6890.171587X-RAY DIFFRACTION10192
4.689-4.8270.171604X-RAY DIFFRACTION10196
4.827-4.9820.191577X-RAY DIFFRACTION10194
4.982-5.160.189580X-RAY DIFFRACTION10194
5.16-5.3660.21594X-RAY DIFFRACTION10195
5.366-5.610.19599X-RAY DIFFRACTION10195
5.61-5.9050.226621X-RAY DIFFRACTION10198
5.905-6.2730.229577X-RAY DIFFRACTION10196
6.273-6.7550.259594X-RAY DIFFRACTION10196
6.755-7.4310.275594X-RAY DIFFRACTION10195
7.431-8.4970.27593X-RAY DIFFRACTION10195
8.497-10.6690.252601X-RAY DIFFRACTION10194
10.669-39.2510.338560X-RAY DIFFRACTION10190

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