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- PDB-7zm6: Nariva virus receptor binding protein -

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Basic information

Entry
Database: PDB / ID: 7zm6
TitleNariva virus receptor binding protein
ComponentsAttachment protein
KeywordsVIRAL PROTEIN / Receptor binding protein / attachment glycoprotein / paramyxovirus
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesNariva narmovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsStelfox, A.J. / Rissanen, I. / Rambo, R. / Lee, B. / Bowden, T.A.
Funding support United Kingdom, Finland, United States, 11items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K503113/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L505031/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/M50659X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/M508111/1 United Kingdom
Academy of Finland#309605 Finland
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123449 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI069317 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115226 United States
Wellcome Trust203141/Z/16Z United Kingdom
CitationJournal: Mbio / Year: 2023
Title: Crystal structure and solution state of the C-terminal head region of the narmovirus receptor binding protein.
Authors: Stelfox, A.J. / Oguntuyo, K.Y. / Rissanen, I. / Harlos, K. / Rambo, R. / Lee, B. / Bowden, T.A.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.2Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment protein
B: Attachment protein


Theoretical massNumber of molelcules
Total (without water)144,9692
Polymers144,9692
Non-polymers00
Water12,989721
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, Size-exclusion chromatography-coupled small-angle X-ray scattering (SEC-SAXS) was performed to assess the oligomerisation state of glycosylated (high mannose) Nariva virus receptor ...Evidence: SAXS, Size-exclusion chromatography-coupled small-angle X-ray scattering (SEC-SAXS) was performed to assess the oligomerisation state of glycosylated (high mannose) Nariva virus receptor binding protein in solution. Using the dimeric crystal structure data a best fitting model was generated using molecular dynamics, which considered the flexibility of the high mannose N-linked glycans and C- and N-termini. The extensive homodimeric interface observed in the crystal structure was largely retained.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.382, 82.957, 92.988
Angle α, β, γ (deg.)90.000, 90.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 198 through 626)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 198 - 626 / Label seq-ID: 198 - 626

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 198 through 626)BB

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Components

#1: Protein Attachment protein


Mass: 72484.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nariva narmovirus
Cell line (production host): Human embryonic kidney 293T cells
Production host: Homo sapiens (human) / References: UniProt: B8XH64
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.5, 25% PEG 3350, 10% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→82.96 Å / Num. obs: 51334 / % possible obs: 100 % / Redundancy: 3.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.13 / Net I/σ(I): 4.2
Reflection shellResolution: 2.07→2.14 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 50856 / CC1/2: 0.62 / Rpim(I) all: 0.59 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Mossman virus receptor binding protein

Resolution: 2.07→61.9278 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 2600 5.11 %
Rwork0.2296 48257 -
obs0.2317 50857 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.81 Å2 / Biso mean: 23.6498 Å2 / Biso min: 4.05 Å2
Refinement stepCycle: final / Resolution: 2.07→61.9278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 0 721 7423
Biso mean---26.58 -
Num. residues----862
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4041X-RAY DIFFRACTION10.147TORSIONAL
12B4041X-RAY DIFFRACTION10.147TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.10770.36491150.3312509262497
2.1077-2.14820.38121180.3362490260898
2.1482-2.19210.38421350.32662492262798
2.1921-2.23970.29271560.31222527268399
2.2397-2.29180.37131570.30892469262699
2.2918-2.34910.37181430.31892510265398
2.3491-2.41270.34971380.30842512265099
2.4127-2.48370.32171420.29222529267199
2.4837-2.56380.3241180.28582566268499
2.5638-2.65550.33611030.27752593269699
2.6555-2.76180.29421510.25692525267699
2.7618-2.88750.26741580.25242493265199
2.8875-3.03970.3141440.226325562700100
3.0397-3.23010.24891280.222125612689100
3.2301-3.47950.21691610.187425492710100
3.4795-3.82960.22151480.169625472695100
3.8296-4.38370.20181170.149325962713100
4.3837-5.52240.18961410.15225972738100
5.5224-61.92780.20631270.184126362763100
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)
10.93540.6196-0.54771.4482-0.48820.9539-0.0028-0.03890.1493-0.01850.11290.31250.0134-0.1177-0.06150.09310.0057-0.02060.15550.01980.233330.416947.333674.0662
20.4370.0240.10981.1556-0.10160.4179-0.0402-0.0188-0.01750.0870.0245-0.16310.0039-0.00680.00880.11670.0094-0.01220.1095-0.00180.206650.442646.947882.7414
31.0136-0.04650.08121.7060.30970.85720.04310.0301-0.14490.1598-0.0169-0.20930.17330.02140.010.17830.0112-0.03830.11210.00510.23454.074626.570284.7337
40.8242-0.41960.36071.2276-0.010.43220.027-0.0216-0.2118-0.0626-0.02060.00780.0643-0.0415-0.02630.1425-0.01-0.01160.1014-0.02090.23243.11628.556177.1805
50.64530.17560.02031.1161-0.15190.48020.01090.03540.0092-0.13170.05780.19710.0666-0.0916-0.06460.1204-0.0105-0.01890.15320.00490.197133.716941.29768.724
60.74270.278-0.00851.6838-0.02780.497-0.013-0.0222-0.14490.0403-0.0282-0.4324-0.09230.06370.08440.1131-0.004-0.02470.17960.01320.306460.192871.322266.6428
70.5181-0.0890.10231.5408-0.34960.753-0.03390.01390.10720.0320.07230.1386-0.0592-0.0739-0.03030.09520.015-0.00280.12580.00470.192437.083975.46769.5719
80.88930.2073-0.54971.3738-0.15210.9454-0.04230.14630.1113-0.19990.10670.098-0.1003-0.15650.00870.1932-0.0129-0.04790.18750.03360.204340.240187.480154.0687
90.620.1448-0.34161.515-0.67450.9567-0.12890.088-0.0624-0.3280.0625-0.30030.02680.09130.00130.1196-0.00230.05330.1333-0.02030.190953.830469.738156.1384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 198 through 240 )A198 - 240
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 393 )A241 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 450 )A394 - 450
4X-RAY DIFFRACTION4chain 'A' and (resid 451 through 535 )A451 - 535
5X-RAY DIFFRACTION5chain 'A' and (resid 536 through 626 )A536 - 626
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 233 )B194 - 233
7X-RAY DIFFRACTION7chain 'B' and (resid 234 through 393 )B234 - 393
8X-RAY DIFFRACTION8chain 'B' and (resid 394 through 535 )B394 - 535
9X-RAY DIFFRACTION9chain 'B' and (resid 536 through 626 )B536 - 626

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