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- PDB-6otn: Crystal Structure of an N-terminal Fragment of Cancer Associated ... -

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Basic information

Entry
Database: PDB / ID: 6otn
TitleCrystal Structure of an N-terminal Fragment of Cancer Associated Tropomyosin 3.1 (Tpm3.1)
ComponentsTropomyosin alpha-3 chain
KeywordsSTRUCTURAL PROTEIN / tropomyosin / fragment / coiled coil
Function / homology
Function and homology information


muscle thin filament tropomyosin / muscle filament sliding / Striated Muscle Contraction / Smooth Muscle Contraction / stress fiber / muscle contraction / actin filament / actin filament organization / actin filament binding / actin cytoskeleton ...muscle thin filament tropomyosin / muscle filament sliding / Striated Muscle Contraction / Smooth Muscle Contraction / stress fiber / muscle contraction / actin filament / actin filament organization / actin filament binding / actin cytoskeleton / cytoskeleton / extracellular exosome / cytosol
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin
Similarity search - Domain/homology
Tropomyosin alpha-3 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsRynkiewicz, M.J. / Ghosh, A. / Lehman, W.J. / Janco, M. / Gunning, P.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1100202 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1079866 Australia
CitationJournal: Sci Rep / Year: 2019
Title: Molecular integration of the anti-tropomyosin compound ATM-3507 into the coiled coil overlap region of the cancer-associated Tpm3.1.
Authors: Janco, M. / Rynkiewicz, M.J. / Li, L. / Hook, J. / Eiffe, E. / Ghosh, A. / Bocking, T. / Lehman, W.J. / Hardeman, E.C. / Gunning, P.W.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tropomyosin alpha-3 chain
B: Tropomyosin alpha-3 chain
C: Tropomyosin alpha-3 chain
D: Tropomyosin alpha-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2375
Polymers37,1414
Non-polymers961
Water1,29772
1
A: Tropomyosin alpha-3 chain
B: Tropomyosin alpha-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6673
Polymers18,5712
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-29 kcal/mol
Surface area10170 Å2
MethodPISA
2
C: Tropomyosin alpha-3 chain
D: Tropomyosin alpha-3 chain


Theoretical massNumber of molelcules
Total (without water)18,5712
Polymers18,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-41 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.201, 97.201, 93.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and resid 6 through 74)
12chain B
22(chain D and resid 12 through 78)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUchain AAA6 - 747 - 75
21THRTHRLEULEU(chain C and resid 6 through 74)CC6 - 747 - 75
12ARGARGGLUGLUchain BBB12 - 7813 - 79
22ARGARGGLUGLU(chain D and resid 12 through 78)DD12 - 7813 - 79

NCS ensembles :
ID
1
2

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Components

#1: Protein
Tropomyosin alpha-3 chain / Gamma-tropomyosin / Tropomyosin-3 / Tropomyosin-5 / hTM5


Mass: 9285.301 Da / Num. of mol.: 4 / Mutation: A80C
Source method: isolated from a genetically manipulated source
Details: The construct contains an N-terminal Ala-Ser followed by residues Ala2-Ala80 of Tpm3.1 with an A80C mutation
Source: (gene. exp.) Homo sapiens (human) / Gene: TPM3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06753
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals were grown in hanging drops by mixing purified N_82AA_Tpm3.1 at 20 mg/ml with an equal volume of reservoir solution (0.1 M BisTris pH 6.5, 0.2 M Li2SO4, 12% polyethylene glycol 3350)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.4→29.56 Å / Num. obs: 17984 / % possible obs: 99.3 % / Redundancy: 15.3 % / Biso Wilson estimate: 48.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.022 / Rrim(I) all: 0.086 / Net I/σ(I): 23.2 / Num. measured all: 274283 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4614.40.7911723711960.9110.2070.8193.490.9
10.72-29.5612.90.03931202420.9990.0110.0458.695.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IC2

1ic2


Resolution: 2.4→29.56 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.36
RfactorNum. reflection% reflection
Rfree0.2658 1765 10.03 %
Rwork0.2348 --
obs0.238 17592 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 208.62 Å2 / Biso mean: 71.6032 Å2 / Biso min: 26.42 Å2
Refinement stepCycle: final / Resolution: 2.4→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 5 72 2388
Biso mean--107.92 53.49 -
Num. residues----282
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A695X-RAY DIFFRACTION10.121TORSIONAL
12C695X-RAY DIFFRACTION10.121TORSIONAL
21B660X-RAY DIFFRACTION10.121TORSIONAL
22D660X-RAY DIFFRACTION10.121TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.46320.34821070.2987104985
2.4632-2.53560.29191430.274113895
2.5356-2.61740.32611200.2622117896
2.6174-2.71090.3131360.2764119297
2.7109-2.81940.33211420.2682120098
2.8194-2.94760.36171290.2715121499
2.9476-3.10280.29541360.2724122299
3.1028-3.2970.34031380.27321245100
3.297-3.55120.30321350.25111244100
3.5512-3.90780.24771460.21361234100
3.9078-4.47160.20311390.18731276100
4.4716-5.62740.22671440.22611273100
5.6274-29.560.22711500.2136136299
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)
10.6237-0.4473-1.41072.79452.43726.8929-0.047-0.01450.0880.01580.05340.06220.3393-0.1962-0.04290.2705-0.02850.00140.38990.03050.466970.722849.107233.3974
20.42340.22390.40853.7323.66729.4434-0.10340.11750.0123-0.0648-0.41890.28950.4458-0.87070.29080.2767-0.03570.03130.42270.01670.433166.457843.938328.5752
31.56490.09730.32650.2556-0.34667.2206-0.01990.09330.1457-0.1588-0.2260.13890.0673-0.09290.13120.34950.0089-0.01570.25340.04860.381280.754252.164819.5083
41.25240.35331.08591.42713.16038.84550.10550.2437-0.1242-0.31950.3423-0.1222-0.83860.5227-0.31030.4138-0.02730.03110.37550.04540.424884.120254.3917.7615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 74 )A6 - 74
2X-RAY DIFFRACTION2chain 'B' and (resid 12 through 78 )B12 - 78
3X-RAY DIFFRACTION3chain 'C' and (resid 6 through 80 )C6 - 80
4X-RAY DIFFRACTION4chain 'D' and (resid 8 through 78 )D8 - 78

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