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- PDB-9h2d: Human IFT172 C-terminal U-box domain crystal structure -

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Basic information

Entry
Database: PDB / ID: 9h2d
TitleHuman IFT172 C-terminal U-box domain crystal structure
ComponentsIntraflagellar transport protein 172 homolog
KeywordsPROTEIN TRANSPORT / Cilia / intraflagellar transport / IFT172 / intracellular trafficking / U-box / ubiquitin
Function / homology
Function and homology information


hindgut development / sperm cytoplasmic droplet / intraciliary anterograde transport / intraciliary transport particle B / embryonic camera-type eye morphogenesis / sperm principal piece / intraciliary transport / spinal cord motor neuron differentiation / left/right axis specification / ciliary tip ...hindgut development / sperm cytoplasmic droplet / intraciliary anterograde transport / intraciliary transport particle B / embryonic camera-type eye morphogenesis / sperm principal piece / intraciliary transport / spinal cord motor neuron differentiation / left/right axis specification / ciliary tip / Intraflagellar transport / non-motile cilium assembly / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / limb development / smoothened signaling pathway / heart looping / roof of mouth development / keratinocyte proliferation / axoneme / cilium assembly / epidermis development / negative regulation of keratinocyte proliferation / Hedgehog 'off' state / Notch signaling pathway / cytoplasmic microtubule organization / sperm midpiece / negative regulation of smoothened signaling pathway / neural tube closure / brain development / protein processing / bone development / extracellular vesicle / ciliary basal body / cilium
Similarity search - Function
Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Intraflagellar transport protein 172 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsLorentzen, E. / Zacharia, N.K. / Bhogaraju, S.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF23OC0085823 Denmark
CitationJournal: To Be Published
Title: Intraflagellar transport protein IFT172 contains a C-terminal ubiquitin-binding U-box-like domain involved in ciliary signaling
Authors: Lorentzen, E. / Zacharia, N.K. / Bhogaraju, S.
History
DepositionOct 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intraflagellar transport protein 172 homolog
B: Intraflagellar transport protein 172 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5515
Polymers61,0392
Non-polymers5123
Water3,189177
1
A: Intraflagellar transport protein 172 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7933
Polymers30,5201
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intraflagellar transport protein 172 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7582
Polymers30,5201
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.967, 90.507, 67.423
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Intraflagellar transport protein 172 homolog


Mass: 30519.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFT172, KIAA1179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UG01
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3350, pH 9.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.006 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.07→46.573 Å / Num. obs: 34038 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 9.7
Reflection shellResolution: 2.07→2.1 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1631 / CC1/2: 0.777 / Rpim(I) all: 0.483 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.097→46.573 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 1564 4.8 %
Rwork0.1893 --
obs0.1917 32557 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65 Å2
Refinement stepCycle: LAST / Resolution: 2.097→46.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 1 177 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084327
X-RAY DIFFRACTIONf_angle_d0.9525904
X-RAY DIFFRACTIONf_dihedral_angle_d6.6823509
X-RAY DIFFRACTIONf_chiral_restr0.05661
X-RAY DIFFRACTIONf_plane_restr0.008768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0972-2.16490.34781340.35252602X-RAY DIFFRACTION92
2.1649-2.24230.39071460.31932827X-RAY DIFFRACTION100
2.2423-2.33210.35841400.28832821X-RAY DIFFRACTION100
2.3321-2.43820.36661510.26412799X-RAY DIFFRACTION100
2.4382-2.56680.30151520.24412835X-RAY DIFFRACTION100
2.5668-2.72760.29051280.21522830X-RAY DIFFRACTION100
2.7276-2.93810.25821420.20482858X-RAY DIFFRACTION100
2.9381-3.23370.30021260.2012838X-RAY DIFFRACTION100
3.2337-3.70150.23961390.18062850X-RAY DIFFRACTION100
3.7015-4.66280.1911490.14042850X-RAY DIFFRACTION100
4.6628-46.5730.17421570.15222883X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.8411 Å / Origin y: -23.3209 Å / Origin z: 17.3765 Å
111213212223313233
T0.33 Å20.0158 Å20.1808 Å2-0.229 Å2-0.0044 Å2--0.706 Å2
L1.2881 °20.1199 °20.4937 °2-1.4107 °20.3594 °2--1.7332 °2
S0.0095 Å °-0.011 Å °0.0163 Å °-0.1413 Å °-0.032 Å °-0.04 Å °-0.1625 Å °0.052 Å °0.0318 Å °
Refinement TLS groupSelection details: all

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