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- PDB-8ahn: Sin Nombre virus Gn in complex with Fab SNV-42 -

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Basic information

Entry
Database: PDB / ID: 8ahn
TitleSin Nombre virus Gn in complex with Fab SNV-42
Components
  • Envelope polyprotein
  • Fab SNV-42 heavy chain
  • Fab SNV-42 light chain
KeywordsVIRAL PROTEIN / Sin Nombre / virus / hantavirus / Fab / SNV-42 / complex
Function / homology
Function and homology information


: / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virion membrane / cell surface / signal transduction ...: / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virion membrane / cell surface / signal transduction / metal ion binding / membrane
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSin Nombre orthohantavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStass, R. / Bowden, T.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V031635/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2023
Title: Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody.
Authors: Stass, R. / Engdahl, T.B. / Chapman, N.S. / Wolters, R.M. / Handal, L.S. / Diaz, S.M. / Crowe Jr., J.E. / Bowden, T.A.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 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: Envelope polyprotein
L: Fab SNV-42 light chain
H: Fab SNV-42 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4805
Polymers85,8353
Non-polymers6462
Water13,709761
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.926, 146.420, 157.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody Fab SNV-42 light chain


Mass: 22906.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab SNV-42 heavy chain


Mass: 23642.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Non-polymers , 2 types, 762 molecules A

#1: Protein Envelope polyprotein / M polyprotein


Mass: 39286.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sin Nombre orthohantavirus / Production host: Homo sapiens (human) / References: UniProt: K9MNN9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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

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Details

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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 0.2 M tri-ammonium citrate pH 7.0 and 20% w/v polyethylene glycol 3350
Temp details: Room temperature

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→46.62 Å / Num. obs: 95210 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rrim(I) all: 0.125 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 14 %

Resolution (Å)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.8-1.831.146820.3791.43499.7
4.88-46.6450.450230.0150.056100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia23.8.0-g3d57088-dials-3.8data scaling
PDB_EXTRACT3.27data extraction
xia23.8.0-g3d57088-dials-3.8data reduction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 5OPG and PDB ID 5UR8

5opg

5ur8


Resolution: 1.8→46.62 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 4846 5.09 %
Rwork0.1895 --
obs0.1911 95137 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 42 761 6421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086018
X-RAY DIFFRACTIONf_angle_d0.9988238
X-RAY DIFFRACTIONf_dihedral_angle_d6.413863
X-RAY DIFFRACTIONf_chiral_restr0.064953
X-RAY DIFFRACTIONf_plane_restr0.0081057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31761380.29612989X-RAY DIFFRACTION100
1.82-1.840.29371710.28122979X-RAY DIFFRACTION100
1.84-1.860.29911360.26972964X-RAY DIFFRACTION100
1.86-1.890.27651470.25773022X-RAY DIFFRACTION100
1.89-1.910.27061620.25532980X-RAY DIFFRACTION100
1.91-1.940.2481650.25562996X-RAY DIFFRACTION100
1.94-1.970.30461600.25422978X-RAY DIFFRACTION100
1.97-20.29481510.24672987X-RAY DIFFRACTION100
2-2.030.25871470.22732989X-RAY DIFFRACTION100
2.03-2.060.24851700.22082990X-RAY DIFFRACTION100
2.06-2.10.26131750.21882958X-RAY DIFFRACTION100
2.1-2.130.23911550.20793007X-RAY DIFFRACTION100
2.13-2.180.24361610.20252990X-RAY DIFFRACTION100
2.18-2.220.2891610.21373013X-RAY DIFFRACTION100
2.22-2.270.25161740.20682967X-RAY DIFFRACTION100
2.27-2.320.25591870.20332982X-RAY DIFFRACTION100
2.32-2.380.27181950.21142981X-RAY DIFFRACTION100
2.38-2.440.24041440.20553000X-RAY DIFFRACTION100
2.44-2.510.21611640.19883012X-RAY DIFFRACTION100
2.51-2.60.25181370.20183025X-RAY DIFFRACTION100
2.6-2.690.23821330.20243034X-RAY DIFFRACTION100
2.69-2.80.24431590.19123014X-RAY DIFFRACTION100
2.8-2.920.23641460.19343042X-RAY DIFFRACTION100
2.92-3.080.23661910.19022992X-RAY DIFFRACTION100
3.08-3.270.20971760.1833000X-RAY DIFFRACTION100
3.27-3.520.21071730.1733040X-RAY DIFFRACTION100
3.52-3.880.21161330.17083088X-RAY DIFFRACTION100
3.88-4.440.16941680.1423049X-RAY DIFFRACTION100
4.44-5.590.15531730.14753091X-RAY DIFFRACTION100
5.59-46.620.20021940.18583132X-RAY DIFFRACTION98
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)
12.22860.22010.01651.07510.51233.4606-0.02790.5653-0.0827-0.19320.10450.120.121-0.4798-0.06880.253-0.0824-0.04550.54010.08650.247570.08841.005-6.941
21.30530.24940.83350.53130.33981.0728-0.0178-0.12430.09070.0587-0.02570.0186-0.0207-0.11290.04760.17620.010.05380.1570.01950.188684.98852.67543.95
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A22 - 128
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A130 - 220
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A230 - 241
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A243 - 303
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A305 - 344
6X-RAY DIFFRACTION2( CHAIN B AND RESID 2:2 )B2

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