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- PDB-1uuj: N-terminal domain of Lissencephaly-1 protein (Lis-1) -

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Basic information

Entry
Database: PDB / ID: 1uuj
TitleN-terminal domain of Lissencephaly-1 protein (Lis-1)
ComponentsPLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
KeywordsCELL DIVISION / PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / MITOSIS / NEUROGENESIS / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


: / ameboidal-type cell migration / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-independent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / platelet-activating factor acetyltransferase activity / Loss of Nlp from mitotic centrosomes ...: / ameboidal-type cell migration / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-independent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / platelet-activating factor acetyltransferase activity / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / maintenance of centrosome location / Regulation of PLK1 Activity at G2/M Transition / Separation of Sister Chromatids / microtubule cytoskeleton organization involved in establishment of planar polarity / positive regulation of cytokine-mediated signaling pathway / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / cerebral cortex neuron differentiation / corpus callosum morphogenesis / COPI-independent Golgi-to-ER retrograde traffic / establishment of centrosome localization / acrosome assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / layer formation in cerebral cortex / central region of growth cone / nuclear membrane disassembly / auditory receptor cell development / microtubule sliding / positive regulation of cellular component organization / osteoclast development / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / neuroblast proliferation / microtubule organizing center organization / positive regulation of embryonic development / brain morphogenesis / RHO GTPases Activate Formins / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Separation of Sister Chromatids / Anchoring of the basal body to the plasma membrane / astral microtubule / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / cortical microtubule organization / reelin-mediated signaling pathway / Regulation of PLK1 Activity at G2/M Transition / positive regulation of dendritic spine morphogenesis / germ cell development / regulation of GTPase activity / stem cell division / neuromuscular process controlling balance / stereocilium / microtubule plus-end binding / motile cilium / vesicle transport along microtubule / retrograde axonal transport / negative regulation of JNK cascade / regulation of postsynapse organization / microtubule associated complex / kinesin complex / nuclear migration / establishment of mitotic spindle orientation / dynein intermediate chain binding / cell leading edge / protein secretion / transmission of nerve impulse / dynein complex binding / cochlea development / positive regulation of axon extension / lipid catabolic process / adult locomotory behavior / microtubule-based process / cytoplasmic microtubule / positive regulation of mitotic cell cycle / axon cytoplasm / sperm midpiece / hippocampus development / brain development / negative regulation of neuron projection development / neuron migration / regulation of microtubule cytoskeleton organization / phosphoprotein binding / cerebral cortex development / microtubule cytoskeleton organization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / kinetochore / microtubule cytoskeleton / actin cytoskeleton organization / nuclear envelope / cell migration / nuclear membrane
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #30 / : / LisH / : / : / PAC1 LisH domain / Dynein regulator LIS1 / LIS1, N-terminal / Mitochondrial Import Receptor Subunit Tom20; Chain A / Lissencephaly type-1-like homology motif ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #30 / : / LisH / : / : / PAC1 LisH domain / Dynein regulator LIS1 / LIS1, N-terminal / Mitochondrial Import Receptor Subunit Tom20; Chain A / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / BENZOIC ACID / Platelet-activating factor acetylhydrolase IB subunit alpha / Platelet-activating factor acetylhydrolase IB subunit beta
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsCooper, D.R. / Kim, M.H. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2004
Title: The Structure of the N-Terminal Domain of the Product of the Lissencephaly Gene Lis1 and its Functional Implications
Authors: Kim, M.H. / Cooper, D.R. / Oleksy, A. / Devedjiev, Y. / Derewenda, U. / Reiner, O. / Otlewski, J. / Derewenda, Z.S.
History
DepositionDec 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3May 29, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
B: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
C: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
D: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,65410
Polymers41,0894
Non-polymers5656
Water3,261181
1
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
B: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7955
Polymers20,5442
Non-polymers2513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
D: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8595
Polymers20,5442
Non-polymers3143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.988, 111.753, 47.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT / LISSENCEPHALY-1 PROTEIN / PAF / PAF-AH ALPHA / ACETYLHYDROLASE 45 KDA SUBUNIT / PAF-AH 45 KDA ...LISSENCEPHALY-1 PROTEIN / PAF / PAF-AH ALPHA / ACETYLHYDROLASE 45 KDA SUBUNIT / PAF-AH 45 KDA SUBUNIT / PAFAH ALPHA / LIS-1


Mass: 10272.154 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN RESIDUES 1-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P43035, UniProt: P63005*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsINITIAL 2 RESIDUES ARE CLONING ARTIFACTS.

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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: 2.1 Å3/Da / Density % sol: 49.6 %
Crystal growMethod: microbatch / pH: 4.5
Details: CRYSTALS WERE GROWN USING SITTING-DROP VAPOUR-DIFFUSION UNDER MINERAL OIL USING A 1:1 MIXTURE OF PROTEIN AND 1.7 M (NH4)2SO4 AND 0.1 M NA3-CITRATE, PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979392,0.979528, 0.964216
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793921
20.9795281
30.9642161
ReflectionResolution: 1.75→50 Å / Num. obs: 33378 / % possible obs: 96.1 % / Redundancy: 12 % / Biso Wilson estimate: 26.88 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 40
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 9 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
SHARPphasing
ARP/wARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.377 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1069 3.2 %RANDOM
Rwork0.19 ---
obs0.192 31827 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 33 181 2772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212612
X-RAY DIFFRACTIONr_bond_other_d0.0020.022371
X-RAY DIFFRACTIONr_angle_refined_deg2.8831.9963481
X-RAY DIFFRACTIONr_angle_other_deg1.59135559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7855303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2380.2612
X-RAY DIFFRACTIONr_nbd_other0.2380.22664
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.21611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1481.51529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18822428
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.60431083
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7564.51053
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 63
Rwork0.245 1792
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)
10.9598-0.81080.43251.9555-1.07041.6349-0.1551-0.16310.15320.33850.11630.0139-0.4126-0.0050.03880.1624-0.00820.00660.04810.00510.067519.45846.3122.361
21.5561-0.35680.34942.1404-0.44511.4081-0.12190.1480.0888-0.19890.12390.0508-0.1489-0.0507-0.0020.0913-0.01870.00270.0730.0310.030918.89140.983-5.795
31.8629-0.74130.07211.6267-0.50970.1528-0.0993-0.2897-0.13410.30270.1495-0.04130.07670.0163-0.05020.1588-0.0104-0.0030.05110.02140.00912.68714.67524.013
40.9477-0.7688-0.1382.1461-0.67820.54930.01310.0304-0.02260.1436-0.0807-0.04310.05570.0210.06760.09140.0003-0.01280.03890.00340.040213.08917.43916.141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 77
2X-RAY DIFFRACTION2B2 - 74
3X-RAY DIFFRACTION3C3 - 76
4X-RAY DIFFRACTION4D1 - 78

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