[English] 日本語
Yorodumi
- PDB-1usx: Crystal structure of the Newcastle disease virus hemagglutinin-ne... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1usx
TitleCrystal structure of the Newcastle disease virus hemagglutinin-neuraminidase complexed with thiosialoside
ComponentsHEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
KeywordsHYDROLASE / NEURAMINIDASE / HEMAGGLUTININ / SIALIDASE
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesNEWCASTLE DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZaitsev, V. / Itzstein, M. / Groves, D. / Kiefel, M. / Takimoto, T. / Portner, A. / Taylor, G.
Citation
Journal: J.Virol. / Year: 2004
Title: Second Sialic Acid Binding Site in Newcastle Disease Virus Hemagglutinin-Neuraminidase: Implications for Fusion
Authors: Zaitsev, V. / Von Itzstein, M. / Groves, D. / Kiefel, M. / Takimoto, T. / Portner, A. / Taylor, G.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal Structure of the Multifunctional Paramyxovirus Hemagglutinin-Neuraminidase
Authors: Crennell, S. / Takimoto, T. / Portner, A. / Taylor, G.
#2: Journal: Virology / Year: 2000
Title: Crystallization of Newcastle Disease Virus Hemagglutinin-Neuraminidase Glycoprotein
Authors: Takimoto, T. / Taylor, G.L. / Crennell, S.J. / Scroggs, R.A. / Portner, A.
History
DepositionDec 1, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Structure summary / Version format compliance
Revision 1.2Mar 4, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.type / _pdbx_struct_assembly_gen.assembly_id ..._chem_comp.type / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[3] / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 1, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn
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_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num / _struct_conn.ptnr2_label_atom_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 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 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
B: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
C: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,9499
Polymers149,5713
Non-polymers2,3786
Water00
1
A: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
B: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2996
Polymers99,7142
Non-polymers1,5864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-27 kcal/mol
Surface area29810 Å2
MethodPISA
2
C: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
hetero molecules

C: HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2996
Polymers99,7142
Non-polymers1,5864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6250 Å2
ΔGint-25 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.070, 115.070, 283.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.70224, 0.7046, 0.10202), (0.70315, -0.70886, 0.05568), (0.11155, 0.03264, -0.99322)
Vector: -0.20411, 0.26087, 0.6262)

-
Components

#1: Protein HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN


Mass: 49856.910 Da / Num. of mol.: 3 / Fragment: HEAD DOMAIN, RESIDUES 124-577 / Source method: isolated from a natural source / Source: (natural) NEWCASTLE DISEASE VIRUS / Strain: KANSAS / References: UniProt: P32884, exo-alpha-sialidase
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-methyl 6-thio-beta-D-galactopyranoside


Type: oligosaccharide / Mass: 501.503 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp6SH]{[(6+S)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17NO8
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
2100 mMthiosialoside1reservoir
30.1 MHEPES1reservoir
420 %PEG33501reservoir
50.1 MHEPES1reservoirpH6.3
62 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2003 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 43065 / % possible obs: 81.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 71.5
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 39099 / % possible obs: 90.4 % / Num. measured all: 454555 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8V

1e8v


Resolution: 2.7→12 Å / Data cutoff high absF: 1000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2095 4 %RANDOM
Rwork0.225 ---
obs0.225 41877 79.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.8 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2--2.07 Å20 Å2
3----4.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10338 0 159 0 10497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more