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- PDB-6jjn: Crystal structure of Mumps virus hemagglutinin-neuraminidase boun... -

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Basic information

Entry
Database: PDB / ID: 6jjn
TitleCrystal structure of Mumps virus hemagglutinin-neuraminidase bound to sialyl lewisX
ComponentsHN protein
KeywordsVIRAL PROTEIN / glycoprotein / beta-propeller / receptor binding / sugar
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 / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMumps rubulavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKubota, M. / Matsuoka, R. / Suzuki, T. / Yonekura, K. / Yanagi, Y. / Hashiguchi, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fk0108014h Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)24115005 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H05820 Japan
CitationJournal: J.Virol. / Year: 2019
Title: Molecular Mechanism of the Flexible Glycan Receptor Recognition by Mumps Virus.
Authors: Kubota, M. / Matsuoka, R. / Suzuki, T. / Yonekura, K. / Yanagi, Y. / Hashiguchi, T.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HN protein
B: HN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,27614
Polymers108,5362
Non-polymers4,74012
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint33 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.417, 137.417, 177.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HN protein / Hemagglutinin-neuraminidase


Mass: 54267.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps rubulavirus / Gene: HN / Production host: Homo sapiens (human) / References: UniProt: Q9WAF5

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Sugars , 3 types, 10 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.: 4
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 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 982.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-1-4/a3-b1_b3-c1_b4-d1_d3-e2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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, 472 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 4.28 Å3/Da / Density % sol: 71.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: sodium acetate, ammonium sulfate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 65599 / % possible obs: 100 % / Redundancy: 20.8 % / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data collection
PHASERphasing
RefinementResolution: 2.5→49.45 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 3457 5.27 %
Rwork0.1743 --
obs0.1759 65599 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 10 470 7842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037600
X-RAY DIFFRACTIONf_angle_d0.68110432
X-RAY DIFFRACTIONf_dihedral_angle_d11.4654442
X-RAY DIFFRACTIONf_chiral_restr0.0471222
X-RAY DIFFRACTIONf_plane_restr0.0051304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.53410.38941320.31272455X-RAY DIFFRACTION100
2.5341-2.57030.3341510.28242448X-RAY DIFFRACTION100
2.5703-2.60870.27121340.24872512X-RAY DIFFRACTION100
2.6087-2.64950.25371400.22592477X-RAY DIFFRACTION100
2.6495-2.69290.25341450.20942461X-RAY DIFFRACTION100
2.6929-2.73930.28721600.19452466X-RAY DIFFRACTION100
2.7393-2.78910.24211610.19282425X-RAY DIFFRACTION100
2.7891-2.84280.23731360.18662519X-RAY DIFFRACTION100
2.8428-2.90080.21151280.18312470X-RAY DIFFRACTION100
2.9008-2.96390.22481290.18892487X-RAY DIFFRACTION100
2.9639-3.03280.18861310.1842506X-RAY DIFFRACTION100
3.0328-3.10860.23721250.19222491X-RAY DIFFRACTION100
3.1086-3.19270.20871510.17782481X-RAY DIFFRACTION100
3.1927-3.28660.21241340.16932480X-RAY DIFFRACTION100
3.2866-3.39270.20091580.16212458X-RAY DIFFRACTION100
3.3927-3.51390.17781200.16612516X-RAY DIFFRACTION100
3.5139-3.65450.19411320.16152481X-RAY DIFFRACTION100
3.6545-3.82080.16551310.15782510X-RAY DIFFRACTION100
3.8208-4.02220.18981660.14972450X-RAY DIFFRACTION100
4.0222-4.2740.1541210.14732513X-RAY DIFFRACTION100
4.274-4.60380.18051380.1382483X-RAY DIFFRACTION100
4.6038-5.06670.17241470.14272493X-RAY DIFFRACTION100
5.0667-5.79890.19851270.15832500X-RAY DIFFRACTION100
5.7989-7.30220.20581220.1832530X-RAY DIFFRACTION100
7.3022-49.45920.18331380.1922530X-RAY DIFFRACTION100
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)
12.5524-1.31820.03091.9453-0.11021.42950.0599-0.28630.17640.10030.08630.078-0.3457-0.2343-0.11470.2630.00190.07930.2459-0.03480.234288.1671153.8349-11.0143
22.19730.83391.86994.6507-0.88213.5616-0.0140.419-0.3787-0.4278-0.1172-0.47520.17850.5230.10740.2467-0.00130.05120.24-0.05550.213599.7357141.7373-23.8154
30.92320.1332-0.02171.4926-0.39511.8139-0.02340.29770.0915-0.36280.12720.09180.0344-0.1164-0.10480.2365-0.02880.02240.30630.01920.249590.6912150.3074-34.3616
41.4042-0.2328-0.26571.6634-0.47992.43730.03970.13320.2974-0.01780.02340.0198-0.40110.0139-0.05270.2623-0.03530.06120.2046-0.00990.288295.6427160.6121-21.9142
51.6204-1.07870.11493.4325-0.19481.5766-0.04620.0115-0.1145-0.17980.1116-0.20630.30390.2167-0.04910.24020.03670.01190.2226-0.05690.2175108.7366121.9016-12.6427
65.3428-0.0620.25891.5854-1.95554.2287-0.0427-0.3320.57330.27580.0134-0.0683-0.66530.0390.08430.24660.01050.06170.2194-0.0480.1998102.7593137.59020.0419
71.7036-0.25760.12310.9251-0.34881.63560.0101-0.4442-0.0730.25550.0363-0.03510.0847-0.0369-0.04470.2505-0.0223-0.00590.3071-0.02570.2316107.051125.872810.7437
81.4011-0.14340.27621.8457-0.25042.13610.0539-0.1058-0.05110.09-0.0721-0.25630.12350.36520.01640.16380.0131-0.00890.3008-0.02220.2706118.222126.0295-1.9704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 438 )
4X-RAY DIFFRACTION4chain 'A' and (resid 439 through 583 )
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 174 )
6X-RAY DIFFRACTION6chain 'B' and (resid 175 through 208 )
7X-RAY DIFFRACTION7chain 'B' and (resid 209 through 438 )
8X-RAY DIFFRACTION8chain 'B' and (resid 439 through 583 )

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