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- PDB-7zm5: Structure of Mossman virus receptor binding protein -

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Basic information

Entry
Database: PDB / ID: 7zm5
TitleStructure of Mossman virus receptor binding protein
ComponentsAttachment glycoprotein
KeywordsVIRAL PROTEIN / Attachment glycoprotein / glycoprotein / receptor binding protein
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Attachment glycoprotein
Similarity search - Component
Biological speciesMossman narmovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.62 Å
AuthorsStelfox, A.J. / Bowden, T.A. / Rissanen, I. / Harlos, K.
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 Finland309605 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
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.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment glycoprotein
B: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,8443
Polymers140,6232
Non-polymers2211
Water12,466692
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) Mossman 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) Mossman 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)80.200, 83.930, 122.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 204 through 631)
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 204 - 631 / Label seq-ID: 204 - 631

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999962989198, 0.00606648240466, 0.00610065780899), (0.00815171301114, 0.89482704962, 0.446338549583), (-0.00275132867039, 0.446371761047, -0.894843383576)Vector: -75. ...NCS oper: (Code: given
Matrix: (-0.999962989198, 0.00606648240466, 0.00610065780899), (0.00815171301114, 0.89482704962, 0.446338549583), (-0.00275132867039, 0.446371761047, -0.894843383576)
Vector: -75.5295936873, 7.38893356796, -30.0642867983)

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Components

#1: Protein Attachment glycoprotein


Mass: 70311.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mossman narmovirus
Cell line (production host): Human embryonic kidney 293T cells
Production host: Homo sapiens (human) / References: UniProt: Q6WGM0
#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.: 1 / Source method: obtained synthetically / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M potassium bromide, 0.2 M potassium thiocynate, 0.1 M sodium cacodylate pH 6.5, 3% PGA-LM, 20% w/v polyethylene glycol (PEG) 550 MME

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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: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→69.17 Å / Num. obs: 105014 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Net I/σ(I): 13
Reflection shellResolution: 1.62→1.65 Å / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10324 / CC1/2: 0.5 / Rpim(I) all: 0.68 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.62→52.38 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 5029 4.79 %
Rwork0.1765 99892 -
obs0.1782 104921 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.82 Å2
Refinement stepCycle: LAST / Resolution: 1.62→52.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 14 692 7472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066946
X-RAY DIFFRACTIONf_angle_d0.88639464
X-RAY DIFFRACTIONf_chiral_restr0.05781063
X-RAY DIFFRACTIONf_plane_restr0.00651226
X-RAY DIFFRACTIONf_dihedral_angle_d12.15282525
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.663009456905 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.38541650.33613266X-RAY DIFFRACTION99.19
1.64-1.660.3551750.32043267X-RAY DIFFRACTION99.28
1.66-1.680.30831560.29643295X-RAY DIFFRACTION99.6
1.68-1.70.30351640.27883277X-RAY DIFFRACTION99.48
1.7-1.720.25821640.2663314X-RAY DIFFRACTION99.86
1.72-1.750.29971590.24513315X-RAY DIFFRACTION99.43
1.75-1.770.27221530.2343276X-RAY DIFFRACTION99.74
1.77-1.80.26851520.22753304X-RAY DIFFRACTION99.77
1.8-1.820.22281650.22553326X-RAY DIFFRACTION99.77
1.82-1.850.27791440.22513302X-RAY DIFFRACTION99.71
1.85-1.890.23981690.21423273X-RAY DIFFRACTION99.62
1.89-1.920.23871860.21243303X-RAY DIFFRACTION99.71
1.92-1.960.2621770.20473326X-RAY DIFFRACTION99.83
1.96-20.23681850.18373278X-RAY DIFFRACTION99.65
2-2.040.21511540.17453316X-RAY DIFFRACTION99.88
2.04-2.090.22841670.16893293X-RAY DIFFRACTION99.88
2.09-2.140.17541520.15983366X-RAY DIFFRACTION99.83
2.14-2.20.20341730.16763274X-RAY DIFFRACTION99.71
2.2-2.260.21071650.18193339X-RAY DIFFRACTION99.94
2.26-2.340.24721540.1843352X-RAY DIFFRACTION99.94
2.34-2.420.21811850.18013317X-RAY DIFFRACTION99.97
2.42-2.520.21081830.17713328X-RAY DIFFRACTION99.86
2.52-2.630.21372120.17293289X-RAY DIFFRACTION99.97
2.63-2.770.21581940.17293333X-RAY DIFFRACTION99.8
2.77-2.940.21291460.17413360X-RAY DIFFRACTION99.91
2.94-3.170.2081470.17433384X-RAY DIFFRACTION99.8
3.17-3.490.19231420.1593438X-RAY DIFFRACTION99.97
3.49-3.990.18991870.15593382X-RAY DIFFRACTION99.89
3.99-5.030.16751850.13813418X-RAY DIFFRACTION99.72
5.03-52.380.20141690.16763581X-RAY DIFFRACTION99.5
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)
13.136205811481.405809222220.448146811282.498934686030.249732911682.350717485570.0540832824627-0.494796412045-0.3844054292250.309403484473-0.135301321249-0.1931131450780.07045893617860.3030080170670.07338406288570.204668201778-0.0178399464917-0.01720470362920.4114912884290.08934356444270.207044961651-16.14876173510.194467658777-1.60380683034
23.554467476090.6281394855330.3215870751621.44234418680.5247056872132.49356756793-0.03762161143380.040398265949-0.183817316819-0.0544404519999-0.05272004077850.0339026161401-0.0325654404190.01479603508690.08769808463810.1548152738220.02287407551430.00357093790570.1013950063710.01530362012280.193192528388-31.3498913773-0.752672894682-17.05209793
33.19284953999-0.1634452052690.6821537219691.62596115366-1.503992731165.318571581770.02051300877450.114779612123-0.0616267469537-0.0343916422659-0.0611154710667-0.03078832502180.089134733152-0.0006673463947740.07216669373370.1169976831710.001248231387630.003394466558530.0793510921397-0.008839383999970.178552258667-31.80924955024.2532795928-18.2543207125
42.760475403040.0493296148961-1.256674215711.47453200367-0.4970332625652.658080846160.1298966772220.1608733270810.279973325594-0.0420840395432-0.00489306784091-0.0411438833377-0.275170432849-0.0112028319967-0.08042297616460.206305161294-0.005803003497850.001836157548540.1326267432220.01890281807120.208919560595-29.116131147310.9696536538-18.9392436707
52.439362737660.176977086191-0.7317194557471.46930698382-0.1716980451252.922660130050.1311680364880.4446473049760.240477415301-0.206894675286-0.0707187673774-0.110951481574-0.3801720435360.133461460383-0.1017602512060.2410404331160.01568840711120.01174819696090.2748977375720.09380336660930.270467272516-22.295423766615.6823112362-30.7240627569
62.2750718688-0.00935237018787-0.7201520463952.51174872578-0.7029866874742.439093928780.06618144108160.4661670004050.146358259087-0.212569246568-0.064685617944-0.2612788893330.009172313244680.476805933323-0.06580913460250.155411337741-0.003360041601250.01146718177220.3463220487910.0538468310930.19367597432-10.38832322158.86836054225-30.8453748148
72.84799583287-1.19379388801-0.480616593746.533355346121.215151552413.141847945140.01197572879950.768346969822-0.509615326213-0.486606469848-0.102896875552-0.1221387619620.2970404376220.5060804626890.08421354887720.2432061395210.07326453075070.05559272271210.590823133102-0.04961740610760.336505830002-7.40049847939-2.49702167451-36.8672730551
83.45793650803-0.2815107439880.03539901952811.24347943265-0.337692685183.496784444850.0621856221850.2118181185650.347608893241-0.0597048853786-0.0825676926213-0.148445298646-0.3317192057370.4298013841690.0009053632315550.180787675111-0.045013430990.02008474494210.2957945841360.06152124198640.234194055605-8.072850172329.41734883345-22.8059055593
93.753946565110.06233358659941.246022853086.170258700571.76498363164.8500103353-0.04615153028240.272151057602-0.310323024683-0.325703996529-0.158085596953-0.357139441575-0.01965208703990.6137588156080.1838869534550.1798072901620.0642901024060.04074480765220.3962488821930.05642866190560.212392352477-6.70074940996-1.43318220854-24.3543061453
102.2961638116-0.313273267705-0.6805792978041.38627466543-0.2971935886193.02430706139-0.06474992440830.222533891362-0.777671161918-0.177366563142-0.1891883698830.03336102412170.6276226072760.2244695154820.2135267995680.3026533340850.1110086070860.05051506316320.28787781291-0.02505064786050.428262835117-11.8201052342-11.1300895154-25.3254682901
113.66456579217-0.1187250758540.1602201076281.54010080364-1.079320088761.89033454143-0.0186596126268-0.184246158481-0.869328133011-0.0810933996047-0.0891271463072-0.2708105630880.38237784260.2559565739640.06260745641670.2390129622670.06291979822230.03980157570060.2224654568390.07350429644870.389332668042-16.2245568985-12.1683832212-12.7054513939
122.55589189230.5901802619790.3321709359322.3106536171.378159951813.733836172570.051266505575-0.291615641631-0.1780399007360.20544804986-0.106719814063-0.03228640490990.1714491081080.2599899396520.0274479470370.1623832719910.0177069481937-0.005207020207560.1945763473610.0729733319970.21374053449-21.0573040446-1.71909475298-8.11069537797
133.999998127710.4260848090643.54835844122.639733502561.046111474368.05098613022-0.01823120635260.0178952371276-0.509933651610.0983697883655-0.107076977522-0.1400982925850.2693921408680.3675681247410.004808944028470.1367921457680.004699935799240.07071763228040.1240826763320.07424570962190.265521690991-25.6167162488-8.22036894708-12.3968156131
143.34979542958-0.0175187885531-0.02929444611091.30856992183-0.5416118404712.588281085010.02813739263590.181071412538-0.0273624777349-0.005075102259140.03351206871770.0464021622011-0.0798173601826-0.186704755333-0.04562126042120.137345968865-0.006701806786350.01024284273690.10835212584-0.01057961238650.154581750772-48.22617246953.9533338461-15.5602434072
153.071649973750.717087661215-0.763139414051.77579115792-0.3108788347811.357316036540.130311670579-0.6203900850830.001922765511130.261619750856-0.1168931693490.0356970681376-0.06993060169030.0621366578273-0.03042680821820.2247635295190.0006614936499880.02167850109320.253063727803-0.02233385429570.154361349246-58.20187554745.103307016063.29287340143
162.5488907751.87944971943-0.07469327646476.184870254220.3911602769381.56652592523-0.00732141369481-0.292518013835-0.2614878177130.1442181589960.01905045383510.07465944047410.0919896988932-0.0616565745878-0.02150496714060.1548525760990.02466200632320.05777689147290.25514762780.03940583778450.188484100793-67.8712435737-5.165362354621.34336437485
172.468384971910.212832938195-0.6762724972720.857532089465-0.1937218592131.16872828175-0.07254749859580.358288062382-0.290052498103-0.08853094979550.02116566516940.05391545898390.161820526176-0.222120652460.02371804053310.176128683538-0.0238610228833-0.0007884602677130.191344366591-0.04031986270680.169427012886-61.0849803018-5.83969634066-16.5719195286
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 203 through 229 )AA203 - 2291 - 27
22chain 'A' and (resid 230 through 258 )AA230 - 25828 - 56
33chain 'A' and (resid 259 through 293 )AA259 - 29357 - 91
44chain 'A' and (resid 294 through 320 )AA294 - 32092 - 118
55chain 'A' and (resid 321 through 371 )AA321 - 371119 - 169
66chain 'A' and (resid 372 through 407 )AA372 - 407170 - 205
77chain 'A' and (resid 408 through 442 )AA408 - 442206 - 240
88chain 'A' and (resid 443 through 482 )AA443 - 482241 - 280
99chain 'A' and (resid 483 through 502 )AA483 - 502281 - 300
1010chain 'A' and (resid 503 through 540 )AA503 - 540301 - 338
1111chain 'A' and (resid 541 through 582 )AA541 - 582339 - 380
1212chain 'A' and (resid 583 through 609 )AA583 - 609381 - 407
1313chain 'A' and (resid 610 through 631 )AA610 - 631408 - 429
1414chain 'B' and (resid 204 through 320 )BC204 - 3201 - 117
1515chain 'B' and (resid 321 through 407 )BC321 - 407118 - 204
1616chain 'B' and (resid 408 through 451 )BC408 - 451205 - 248
1717chain 'B' and (resid 452 through 631 )BC452 - 631249 - 428

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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

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