[English] 日本語
Yorodumi
- PDB-3alw: Crystal structure of the measles virus hemagglutinin bound to its... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3alw
TitleCrystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (Form I, MV-H-SLAM(N102H/R108Y) fusion)
ComponentsHemagglutinin, CDw150
Keywordsviral protein/membrane protein / viral protein-receptor complex / six-bladed beta-propeller fold / Immunoglobulin fold / beta-sandwich / viral protein-membrane protein complex
Function / homology
Function and homology information


lymphocyte activation / signaling receptor activity / host cell surface receptor binding / receptor ligand activity / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface ...lymphocyte activation / signaling receptor activity / host cell surface receptor binding / receptor ligand activity / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / membrane / plasma membrane
Similarity search - Function
Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / : / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase ...Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / : / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin glycoprotein / Hemagglutinin glycoprotein / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesMeasles virus
synthetic construct (others)
Saguinus oedipus (cotton-top tamarin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsHashiguchi, T. / Ose, T. / Kubota, M. / Maita, N. / Kamishikiryo, J. / Maenaka, K. / Yanagi, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM
Authors: Hashiguchi, T. / Ose, T. / Kubota, M. / Maita, N. / Kamishikiryo, J. / Maenaka, K. / Yanagi, Y.
History
DepositionAug 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin, CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5213
Polymers62,0791
Non-polymers4422
Water00
1
A: Hemagglutinin, CDw150
hetero molecules

A: Hemagglutinin, CDw150
hetero molecules

A: Hemagglutinin, CDw150
hetero molecules

A: Hemagglutinin, CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,08512
Polymers248,3154
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
2
A: Hemagglutinin, CDw150
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)375,12718
Polymers372,4736
Non-polymers2,65412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area10210 Å2
ΔGint-71 kcal/mol
Surface area123990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.912, 209.912, 180.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Hemagglutinin, CDw150 / CD150 / Signaling lymphocytic activation molecule 1


Mass: 62078.816 Da / Num. of mol.: 1
Fragment: Hemagglutinin head domain/CD150 V domain, UNP reisudes 30-140
Mutation: N692H, R698Y (CDw150)
Source method: isolated from a genetically manipulated source
Details: MV-H/SLAM fusion protein
Source: (gene. exp.) Measles virus, (gene. exp.) synthetic construct (others), (gene. exp.) Saguinus oedipus (cotton-top tamarin)
Strain: Edmonston B, B95a / Gene: Hemagglutinin, CD150 / Plasmid: pCA7 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human)
References: UniProt: E2RZS2, UniProt: Q9GJT3, UniProt: P08362*PLUS
#2: 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
Has protein modificationY
Sequence detailsTHE GGGSGGGSGGGS(RESIDUES 608-619) AT THE MIDDLE OF THE SEQUENCE IS LINKER REGION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 9.990449 Å3/Da / Density % sol: 87.68824 %
Crystal growTemperature: 293 K / Method: vapor diffusion, floating drop / pH: 5.8
Details: 0.1M imidazole pH5.8, 0.5M (NH4)2SO4, 0.7M Li2SO4, 3% ethylene glycol, VAPOR DIFFUSION, FLOATING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.55→30 Å / Num. obs: 28716 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 38.6
Reflection shellResolution: 3.55→3.68 Å / Redundancy: 20 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 6.5 / Num. unique all: 2831 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZB6

2zb6


Resolution: 3.55→29.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4911388.71 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1447 5.1 %RANDOM
Rwork0.25 ---
obs0.25 28487 98.8 %-
all-28894 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 99.3884 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 138.9 Å2
Baniso -1Baniso -2Baniso -3
1-13.37 Å2-0 Å20 Å2
2--13.37 Å20 Å2
3----26.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.55→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 28 0 4033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
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
LS refinement shellResolution: 3.55→3.68 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 147 5.2 %
Rwork0.342 2661 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

+
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