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- PDB-3alx: Crystal structure of the measles virus hemagglutinin bound to its... -

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Basic information

Entry
Database: PDB / ID: 3alx
TitleCrystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion)
ComponentsHemagglutinin,LINKER,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 / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / 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 / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesMeasles morbillivirus
synthetic construct (others)
Saguinus oedipus (cotton-top tamarin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_name_com.name / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin,LINKER,CDw150
B: Hemagglutinin,LINKER,CDw150
C: Hemagglutinin,LINKER,CDw150
D: Hemagglutinin,LINKER,CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,81910
Polymers248,4914
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-47 kcal/mol
Surface area86300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.713, 170.074, 110.681
Angle α, β, γ (deg.)90.00, 117.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 62122.855 Da / Num. of mol.: 4
Fragment: Hemagglutinin head domain,CD150 V domain, UNP reisudes 30-140
Mutation: L482R(MV-H)/N102H, R108Y(SLAM),L482R(MV-H)/N102H, R108Y(SLAM)
Source method: isolated from a genetically manipulated source
Details: MV-H/SLAM fusion protein
Source: (gene. exp.) Measles morbillivirus, (gene. exp.) synthetic construct (others), (gene. exp.) Saguinus oedipus (cotton-top tamarin)
Plasmid: pCA7 / Gene: CDw150 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human) / References: UniProt: E2RZS2, UniProt: Q9GJT3
#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.: 6
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

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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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, floating drop / pH: 8.3
Details: 0.1M imidazole pH8.3, 0.5M (NH4)2SO4, 0.7M Li2SO4, 0.05M Li(AcO)2, 1% ethylene glycol, vapor diffusion, floating drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 55721 / Num. obs: 52457 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.3
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5246 / % possible all: 98.8

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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: 3.15→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4656519.52 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2644 5 %RANDOM
Rwork0.231 ---
obs0.231 52452 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.5979 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 70.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.65 Å20 Å2-18.01 Å2
2---2.36 Å20 Å2
3----12.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.15→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16229 0 84 0 16313
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_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
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: 3.15→3.35 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 404 4.8 %
Rwork0.305 7967 -
obs--94.5 %
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

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