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- PDB-8dzv: Chicken anti-cardiac Troponin I antibody in complex with peptide -

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Basic information

Entry
Database: PDB / ID: 8dzv
TitleChicken anti-cardiac Troponin I antibody in complex with peptide
Components
  • cTnI peptide
  • scfv 2B12
KeywordsPROTEIN BINDING / scFv / chicken / cTnI / complex
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin T binding / troponin C binding / cardiac Troponin complex / cardiac myofibril / regulation of smooth muscle contraction / troponin complex / negative regulation of ATP-dependent activity / Striated Muscle Contraction / regulation of cardiac muscle contraction by calcium ion signaling ...regulation of systemic arterial blood pressure by ischemic conditions / troponin T binding / troponin C binding / cardiac Troponin complex / cardiac myofibril / regulation of smooth muscle contraction / troponin complex / negative regulation of ATP-dependent activity / Striated Muscle Contraction / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / heart contraction / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / cardiac muscle contraction / Ion homeostasis / sarcomere / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / actin binding / heart development / protein domain specific binding / protein kinase binding / cytosol
Similarity search - Function
Troponin I residues 1-32 / Troponin I residues 1-32 / Troponin / Troponin domain superfamily / Troponin
Similarity search - Domain/homology
: / PHOSPHATE ION / Troponin I, cardiac muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsConroy, P.J. / Law, H.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Design of Polarity-Dependent Immunosensors Based on the Structural Analysis of Engineered Antibodies.
Authors: Islam, J. / Conroy, P. / Fercher, C. / Kim, M. / Yaari, Z. / Jones, M. / Bell, T.D.M. / Caradoc-Davies, T. / Law, R. / Whisstock, J. / Heller, D. / Mahler, S. / Corrie, S.
History
DepositionAug 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scfv 2B12
C: cTnI peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2875
Polymers30,1142
Non-polymers1733
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-10 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.800, 74.210, 75.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody scfv 2B12


Mass: 28623.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide cTnI peptide


Mass: 1489.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19429
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.2 M potassium iodide, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953689 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953689 Å / Relative weight: 1
ReflectionResolution: 1.2→37.72 Å / Num. obs: 80289 / % possible obs: 99.04 % / Redundancy: 1.9 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03426 / Rpim(I) all: 0.03426 / Rrim(I) all: 0.04845 / Net I/σ(I): 14.2
Reflection shellResolution: 1.2→1.243 Å / Rmerge(I) obs: 0.1618 / Num. unique obs: 8013 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.1618 / Rrim(I) all: 0.2289 / % possible all: 88.78

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p48

4p48


Resolution: 1.2→37.72 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1736 4047 5.04 %
Rwork0.1608 76241 -
obs0.1615 80288 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.45 Å2 / Biso mean: 13.8491 Å2 / Biso min: 1.68 Å2
Refinement stepCycle: final / Resolution: 1.2→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 7 448 2260
Biso mean--19.6 25.94 -
Num. residues----247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.1891290.19032645277499
1.21-1.230.19281250.181826072732100
1.23-1.240.23251220.178426352757100
1.24-1.260.17361390.170926282767100
1.26-1.280.18781660.176825892755100
1.28-1.30.18851450.183526102755100
1.3-1.320.18981320.178326282760100
1.32-1.340.20441270.168526332760100
1.34-1.360.19051690.16526152784100
1.36-1.380.17161420.167526012743100
1.38-1.410.19561340.157326462780100
1.41-1.430.16531550.160226092764100
1.43-1.460.1661270.159326262753100
1.46-1.490.17571300.154826642794100
1.49-1.530.18271340.147326372771100
1.53-1.570.14071310.150826182749100
1.57-1.610.16161490.147626322781100
1.61-1.660.16361320.145226352767100
1.66-1.710.19011270.150326672794100
1.71-1.770.15561370.150126592796100
1.77-1.840.16151440.15292618276299
1.84-1.930.17371520.16242633278599
1.93-2.030.14681480.152630277899
2.03-2.160.1691570.14482640279799
2.16-2.320.20271270.16082638276598
2.32-2.560.17361590.16742633279298
2.56-2.930.17541250.16832635276097
2.93-3.690.16861430.15912639278296
3.69-37.720.17121400.16852591273190
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)
11.28680.29070.9270.61260.07321.8860.0623-0.0012-0.05830.0175-0.0211-0.11130.06980.1139-0.03470.04910.0073-0.00760.053-0.00090.0661335.524585.178992.2041
20.4108-0.1243-0.08490.6081-0.04910.87350.0220.00370.0181-0.0112-0.00730.0109-0.0906-0.0305-0.01130.0589-0.00290.00080.04850.00080.0457320.368298.39690.4771
36.75130.4782-0.0045.716-0.24975.3522-0.00440.1984-0.1769-0.19630.00130.33290.1277-0.3398-0.02740.0843-0.0023-0.01310.0663-0.01230.0476319.389787.958775.1514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )A1 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 252 )A91 - 252
3X-RAY DIFFRACTION3chain 'C' and (resid 40 through 51 )C40 - 51

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