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- PDB-6sg8: Structure of Sosuga virus receptor binding protein -

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Basic information

Entry
Database: PDB / ID: 6sg8
TitleStructure of Sosuga virus receptor binding protein
ComponentsHemagglutinin-neuraminidase
KeywordsVIRAL PROTEIN / Receptor binding protein / glycoprotein / attachment glycoprotein / sosuga virus / paramyxovirus / RBP / pararubulavirus
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 / metal ion binding / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
ACETATE ION / Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesSosuga virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBowden, T.A. / Stelfox, A.J.
Funding support United Kingdom, United States, 8items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (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
Wellcome Trust203141/Z/16/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI123449 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A structure-based rationale for sialic acid independent host-cell entry of Sosuga virus.
Authors: Stelfox, A.J. / Bowden, T.A.
History
DepositionAug 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 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

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Assembly

Deposited unit
A: Hemagglutinin-neuraminidase
B: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,65024
Polymers103,7682
Non-polymers2,88322
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-5 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 84.040, 81.690
Angle α, β, γ (deg.)90.000, 112.850, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 157 through 463 or resid 480...A157 - 337
121(chain 'A' and (resid 157 through 463 or resid 480...A375 - 462
131(chain 'A' and (resid 157 through 463 or resid 480...A480 - 493
141(chain 'A' and (resid 157 through 463 or resid 480...A499 - 586
251(chain 'B' and (resid 157 through 337 or resid 375...B157 - 337
261(chain 'B' and (resid 157 through 337 or resid 375...B375 - 462
271(chain 'B' and (resid 157 through 337 or resid 375...B480 - 493
281(chain 'B' and (resid 157 through 337 or resid 375...B499 - 582
291(chain 'B' and (resid 157 through 337 or resid 375...B598 - 601

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Components

#1: Protein Hemagglutinin-neuraminidase


Mass: 51883.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sosuga virus / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: W5SB61
#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.: 10
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
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate pH 6.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→51.6 Å / Num. obs: 32731 / % possible obs: 99.67 % / Redundancy: 6.7 % / Biso Wilson estimate: 63.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 32699 / CC1/2: 0.8 / Rpim(I) all: 0.392 / Rrim(I) all: 1.021 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5b2c

5b2c


Resolution: 2.5→51.6 Å / SU ML: 0.3449 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 1531 4.68 %random selection
Rwork0.1941 31169 --
obs0.1958 32700 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5870 0 182 39 6091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336172
X-RAY DIFFRACTIONf_angle_d0.65278366
X-RAY DIFFRACTIONf_chiral_restr0.0462970
X-RAY DIFFRACTIONf_plane_restr0.0041066
X-RAY DIFFRACTIONf_dihedral_angle_d10.32253696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.35981240.32222810X-RAY DIFFRACTION99.16
2.58-2.670.32251470.27482781X-RAY DIFFRACTION99.39
2.67-2.780.31171450.26252833X-RAY DIFFRACTION99.77
2.78-2.910.29891780.25572791X-RAY DIFFRACTION99.63
2.91-3.060.28721550.23792792X-RAY DIFFRACTION99.7
3.06-3.250.22661250.21632840X-RAY DIFFRACTION99.97
3.25-3.50.24981260.20012828X-RAY DIFFRACTION99.66
3.5-3.850.28171250.19712853X-RAY DIFFRACTION99.87
3.85-4.410.20291250.16662869X-RAY DIFFRACTION99.97
4.41-5.560.16851320.15272875X-RAY DIFFRACTION99.83
5.56-51.60.21421490.19082897X-RAY DIFFRACTION99.64
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)
13.23245696471-0.644975865152-0.1991482271571.43304320593-0.2091049202232.76232033406-0.02566407090160.2879867623460.209384471147-0.06327114023770.1368339285580.0206325528561-0.539864748204-0.242959469231-0.08564363069160.609161748223-0.0942634009431-0.01890278703090.488931642226-0.0173681386130.61189629887539.533354985241.81306853857.41430709269
24.778727984550.883082493222-0.09437464170773.20270233120.1829505684342.336798605210.03587706199110.02747534718590.2040535207610.0150743820757-0.05899707709520.296878752644-0.535596340291-0.487178243020.03986704900060.5770843185680.1232515368390.01001364605810.57862714171-0.03233079163040.67340420398321.373525820942.471332870610.1470810069
36.02868992709-0.407354558393-0.2554380308562.293070823280.8428678374234.72946345737-0.05339280764210.8126657554990.328528724396-0.524940643017-0.03680352186250.449761686369-0.437877827269-0.67656570860.09165550248670.693423434320.0806982445241-0.1484613930680.753064706860.0659869843880.68794913801120.447976449241.9240400799-5.63150705504
43.53833599082-0.2727264793491.450845323272.68246905713-0.5188064945124.665670365090.1001795478120.7769780982630.00179423797055-0.3281783455370.111814806569-0.0232868079250.02013171533270.281377403136-0.171405445150.52365389596-0.02082231704550.02694950682510.633617326192-0.05950614297560.54737577142939.832581128437.1915360066-3.15865485612
52.54580802883-0.1004746839510.6812376291351.03239414809-0.3095041200632.55658315753-0.0822726694119-0.232596383651-0.02779038774690.08894373098720.01537896730320.0669699858358-0.3313207074220.1427787537390.06694633940720.579699241420.0296442982584-0.008285869475040.5019232775540.02423922068620.70129489391847.230516669537.481315520325.6842631395
63.99021446346-1.294166735760.0242851090863.421551051770.4680698605333.14436722976-0.03301026786570.2846528768170.140191385740.0081458971479-0.0828909866194-0.315693856642-0.3064581673310.2373135555320.08963662325030.506160518043-0.0786292071509-0.03340064919430.4775431345180.004814950808180.64383170568463.582803647340.457595471621.4152566847
73.468444095610.6566617256210.02799543586962.431552516270.1048916374672.329186246390.0822344515762-0.175316922358-0.3183565003630.2979886770250.00831829630326-0.5509823914180.2032110224330.47427816675-0.07739490195240.6612589585390.010072164403-0.1410028411850.6291934490740.04124497818320.78304221213969.24141751631.354572128736.0065868505
87.480692880061.884070335111.852599972894.349469478850.04530192062565.02476136110.356935793815-1.32497440216-0.3007720655831.552377232450.0673181993731-0.646155973240.6533879747140.261571313161-0.4992965597930.9626053384710.0216556537704-0.2253793087560.7890797601830.09046839866080.84544346551254.462575095127.55397886443.5798867718
93.432945027410.6918376838790.4648341268773.04724871092-0.6910384455414.849452866560.181232707786-0.453655554617-0.2900287985830.05598500700640.08832359649470.1257396225090.125184014224-0.220324023228-0.1963711297320.385883164398-0.00468092366244-0.02439669869350.4067483344010.07377514196560.59855985997345.641471591729.302923237430.4969466359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 157 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 375 )
3X-RAY DIFFRACTION3chain 'A' and (resid 376 through 489 )
4X-RAY DIFFRACTION4chain 'A' and (resid 490 through 582 )
5X-RAY DIFFRACTION5chain 'B' and (resid 156 through 191 )
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 318 )
7X-RAY DIFFRACTION7chain 'B' and (resid 319 through 489 )
8X-RAY DIFFRACTION8chain 'B' and (resid 490 through 510 )
9X-RAY DIFFRACTION9chain 'B' and (resid 511 through 582 )

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