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- PDB-5fmu: MmIFT54 CH-domain -

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Basic information

Entry
Database: PDB / ID: 5fmu
TitleMmIFT54 CH-domain
ComponentsTRAF3-INTERACTING PROTEIN 1
KeywordsPROTEIN TRANSPORT / CALPONIN HOMOLOGY DOMAIN / IFT / TUBULIN-BINDING DOMAIN / TRAF3IP1 / MIP-T3
Function / homology
Function and homology information


intraciliary anterograde transport / intraciliary transport particle B / Intraflagellar transport / neural tube patterning / negative regulation of defense response to virus / embryonic camera-type eye development / intraciliary transport / ciliary transition zone / ciliary tip / morphogenesis of a polarized epithelium ...intraciliary anterograde transport / intraciliary transport particle B / Intraflagellar transport / neural tube patterning / negative regulation of defense response to virus / embryonic camera-type eye development / intraciliary transport / ciliary transition zone / ciliary tip / morphogenesis of a polarized epithelium / post-anal tail morphogenesis / negative regulation of interferon-beta production / embryonic heart tube development / embryonic digit morphogenesis / ciliary base / axoneme / cilium assembly / tubulin binding / regulation of microtubule cytoskeleton organization / kidney development / negative regulation of smoothened signaling pathway / microtubule cytoskeleton / microtubule binding / defense response to virus / ciliary basal body / cilium / signaling receptor binding / centrosome / negative regulation of transcription by RNA polymerase II / cytosol
Similarity search - Function
Microtubule-binding protein MIP-T3 / TRAF3-interacting protein 1, N-terminal / TRAF3-interacting protein 1, C-terminal domain / TRAF3-interacting protein 1, N-terminal domain superfamily / Microtubule-binding protein MIP-T3 CH-like domain / Microtubule-binding protein MIP-T3 C-terminal region / TRAF3-interacting protein 1 / Actin-binding Protein, T-fimbrin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRAF3-interacting protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.593 Å
AuthorsWeber, K. / Lorentzen, E.
CitationJournal: Embo J. / Year: 2016
Title: Intraflagellar Transport Proteins 172, 80, 57, 54, 38, and 20 Form a Stable Tubulin-Binding Ift-B2 Complex.
Authors: Taschner, M. / Weber, K. / Mourao, A. / Vetter, M. / Awasthi, M. / Stiegler, M. / Bhogaraju, S. / Lorentzen, E.
History
DepositionNov 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAF3-INTERACTING PROTEIN 1
B: TRAF3-INTERACTING PROTEIN 1
C: TRAF3-INTERACTING PROTEIN 1
D: TRAF3-INTERACTING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6985
Polymers60,5034
Non-polymers1951
Water7,800433
1
A: TRAF3-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,1261
Polymers15,1261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAF3-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,1261
Polymers15,1261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRAF3-INTERACTING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3212
Polymers15,1261
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRAF3-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,1261
Polymers15,1261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.930, 59.390, 61.180
Angle α, β, γ (deg.)109.17, 105.15, 89.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TRAF3-INTERACTING PROTEIN 1 / INTRAFLAGELLAR TRANSPORT PROTEIN 54 HOMOLOG / MICROTUBULE-IN TERACTING PROTEIN ASSOCIATED WITH ...INTRAFLAGELLAR TRANSPORT PROTEIN 54 HOMOLOG / MICROTUBULE-IN TERACTING PROTEIN ASSOCIATED WITH TRAF3 / MIP-T3 / MMIFT54 CH-DOMAIN


Mass: 15125.798 Da / Num. of mol.: 4 / Fragment: TUBULIN-BINDING DOMAIN, RESIDUES 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q149C2
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE
Crystal growDetails: 50MM MES PH 5.8, 200MM AMMONIUM ACETATE, 4% MPD, 32%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.593→36.47 Å / Num. obs: 60996 / % possible obs: 93.9 % / Observed criterion σ(I): 1.6 / Redundancy: 2.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.45
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.59 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FMT

5fmt


Resolution: 1.593→36.471 Å / SU ML: 0.18 / σ(F): 1.96 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 1226 2.01 %
Rwork0.1829 --
obs0.1836 60975 94.09 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.593→36.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 12 433 4439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074142
X-RAY DIFFRACTIONf_angle_d0.9915600
X-RAY DIFFRACTIONf_dihedral_angle_d11.8941631
X-RAY DIFFRACTIONf_chiral_restr0.038672
X-RAY DIFFRACTIONf_plane_restr0.004710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5935-1.65730.31181160.28886143X-RAY DIFFRACTION86
1.6573-1.73270.29241460.26656566X-RAY DIFFRACTION94
1.7327-1.82410.28781360.2336616X-RAY DIFFRACTION94
1.8241-1.93840.2391320.20686708X-RAY DIFFRACTION95
1.9384-2.0880.2451430.196770X-RAY DIFFRACTION96
2.088-2.29810.19561310.17886734X-RAY DIFFRACTION96
2.2981-2.63060.20291460.1826784X-RAY DIFFRACTION96
2.6306-3.31390.21151380.17656721X-RAY DIFFRACTION95
3.3139-36.48090.18731380.15636707X-RAY DIFFRACTION95

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