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- PDB-8r40: Crystal structure of diabody CR57 in complex with rabies virus pr... -

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Basic information

Entry
Database: PDB / ID: 8r40
TitleCrystal structure of diabody CR57 in complex with rabies virus protein G domain III
Components
  • Glycoprotein
  • Homospecific Diabody CR57
KeywordsVIRAL PROTEIN / Rabies glycoprotein / antibody-antigen complex / CR57 diabody / antibody / engineered antibody
Function / homology
Function and homology information


viral envelope / virion membrane / membrane
Similarity search - Function
: / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Rabies virus CVS-11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKedari, A. / Rissanen, I.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland#342988 and #346508 Finland
University of Helsinki Finland
Finnish Cultural Foundation#00240631 Finland
CitationJournal: Structure / Year: 2024
Title: Structural insight into rabies virus neutralization revealed by an engineered antibody scaffold.
Authors: Kedari, A. / Iheozor-Ejiofor, R. / Salminen, P. / Ugurlu, H. / Makela, A.R. / Levanov, L. / Vapalahti, O. / Hytonen, V.P. / Saksela, K. / Rissanen, I.
History
DepositionNov 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Dec 18, 2024Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Homospecific Diabody CR57
A: Homospecific Diabody CR57
G: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5918
Polymers83,2234
Non-polymers3684
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, THe complex elutes as a hetero-tetramer comprised of the diabody (dimer) and two copies of bound domain III antigen
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-45 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 69.720, 190.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2

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Components

#1: Antibody Homospecific Diabody CR57


Mass: 28057.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Protein Glycoprotein


Mass: 13553.423 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus CVS-11 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: O92284
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Crystallized in condition containing 0.1 M calcium chloride, 0.1 M imidazole pH 6.5, 10 % (v/v) 2-propanol and 30 % (w/v) PEG1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.7→65.48 Å / Num. obs: 21737 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 66.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.04 / Net I/σ(I): 13.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1067 / CC1/2: 0.689 / Rpim(I) all: 0.392

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia23.10.1data reduction
xia23.10.1data scaling
PHENIX1.19rc6-4061phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→56.28 Å / SU ML: 0.3863 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 1111 5.11 %
Rwork0.2169 20626 -
obs0.2191 21737 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→56.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 24 0 4973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195076
X-RAY DIFFRACTIONf_angle_d0.51176861
X-RAY DIFFRACTIONf_chiral_restr0.0398737
X-RAY DIFFRACTIONf_plane_restr0.0033880
X-RAY DIFFRACTIONf_dihedral_angle_d4.2226717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.40191450.31452508X-RAY DIFFRACTION100
2.82-2.970.32311230.26872539X-RAY DIFFRACTION100
2.97-3.160.28441260.24752566X-RAY DIFFRACTION100
3.16-3.40.29531380.25032529X-RAY DIFFRACTION100
3.4-3.740.2491460.2182547X-RAY DIFFRACTION100
3.74-4.290.24861400.20062578X-RAY DIFFRACTION100
4.29-5.40.22251420.18062617X-RAY DIFFRACTION100
5.4-56.280.24971510.21592742X-RAY DIFFRACTION99.76
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)
11.010840180071.434435278760.361253770126.619621077912.415792987961.853864257930.005139071154310.193661766077-0.06014270124750.477119384280.0836632816251-0.778910579526-0.003851766780830.473363113457-0.06291955012960.418684556750.0560782710479-0.1560408893780.6773922498940.04057673128910.675301969584-1.04681507165-25.4265666439-27.1856146625
23.022087030581.32810253113-1.056941692923.97954622023-2.729172380948.202739682830.04991548503770.02730664993130.0613964588188-0.05131164601050.0326540084735-0.0369115782633-0.008228973234340.0650500832791-0.0347240598260.3242321387140.01040672359690.06045716717420.341893605312-0.01115728108770.484455949761-12.6848231194-56.3416902508-37.8528137799
32.52061187090.38648389604-1.091729744096.6165939291-0.3244664965696.037786482640.285311979849-0.02412194601490.1796010502250.305132846476-0.1323131510980.301696262374-0.32860497324-0.359799569393-0.09307824881250.3644522003510.02031140734780.1682702232790.4200164057370.01376298571960.521242703955-29.8486238691-47.0247415253-26.9258367129
45.97273739084-4.593238358872.390770027176.12735895766-2.809029195047.633385244480.419297403847-0.0346505212095-0.301107532009-0.414022288373-0.9621224535620.5718673557131.41624633596-0.3006551951230.3196032956590.713400088844-0.1501005475720.1319874639840.448256172538-0.05641912683850.59981200492-26.7367281999-60.4346991591-31.4798781027
53.209115173821.462454485241.534119030014.03707982090.8422938712263.30220564383-0.116324877580.1274689469640.2496819903550.1413792580280.04022245902390.190064997095-0.07044948181320.1914839585820.09692255166840.4226362581640.00457140556324-0.02916759355050.5033182273720.02342142774190.472216328375-16.4341407558-16.8160345854-38.1063559596
69.449782889771.39221260711-0.231137912429.51860220818-6.552816593354.68697250040.781875214040.572500435417-0.4474742566511.15165654022-0.437954759433-1.029100909770.645734387360.489209604511-0.4313779412011.151323959780.0232619913377-0.3408164271740.653350420664-0.114339870151.175973714911.1847270083-14.0990578262-9.8726047229
75.3954567189-4.123618373772.259448373425.78353410587-6.580612092439.833508938160.0365566617810.9357110660220.148266987001-0.3683313064080.4463577997390.7226669732960.1834432902380.752617282171-0.4702067802570.878989189949-0.165648099382-0.3628441246870.823150991937-0.1267795355680.8591778919968.36390544991-9.17298156687-13.9728077845
82.151864557152.73887101589-0.2878709795527.335169291430.5889430374377.15130672677-0.3582657451690.5967326718640.1884419009180.912601047487-0.4891973357140.042397619613-0.5757654811640.5017001509250.6396450543910.884399400664-0.00271237156879-0.3178789068380.7422487441110.08395332021820.6674308313439.34113247245-6.58231525823-5.18610300575
92.981452277781.28491105224-3.834005243525.04868669890.3901728336566.03432119225-0.368891653743-0.1172348284140.9560752975720.5885820880560.5947411245980.386905221290.829122408716-0.450373589176-0.2843409617980.818228368167-0.00872867751831-0.2407842011970.714367144238-0.1397023166720.778512049867-2.15834105187-6.59705469513-12.4364913116
104.19489787533-2.80114910612-3.470655498823.974383195592.571749344993.034881412940.1229756713090.4482930146080.211726454133-0.4687836788210.03235092057340.203504791604-0.00897417586584-0.475021731333-0.3786494905940.903673097694-0.1684161842580.1634452391420.8918943990680.1115481468780.961116485044-36.4216505839-60.1076036988-9.60629900983
116.40434865462-3.62632490314-4.671069035618.594467533072.649389858978.28165438852-0.778168000616-1.00960231279-0.658269120380.4771725911150.1376141733760.306256760524-0.3327378615650.9716831782050.6207504641050.745193723081-0.06070506431060.1165579280280.6171914027980.1502919658360.597142153804-27.6492048901-61.3500597487-7.34117174294
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'R' and (resid 2 through 135 )RA2 - 1351 - 134
22chain 'R' and (resid 136 through 241 )RA136 - 241135 - 240
33chain 'A' and (resid -1 through 100 )AB-1 - 1001 - 102
44chain 'A' and (resid 101 through 120 )AB101 - 120103 - 122
55chain 'A' and (resid 121 through 240 )AB121 - 240123 - 242
66chain 'G' and (resid 34 through 46 )GC34 - 461 - 13
77chain 'G' and (resid 47 through 210 )GC47 - 21014 - 42
88chain 'G' and (resid 211 through 222 )GC211 - 22243 - 54
99chain 'G' and (resid 223 through 255 )GC223 - 25555 - 85
1010chain 'C' and (resid 34 through 210 )CD34 - 2101 - 44
1111chain 'C' and (resid 211 through 255 )CD211 - 25545 - 89

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