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- PDB-3mdb: Crystal structure of the ternary complex of full length centaurin... -

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Basic information

Entry
Database: PDB / ID: 3mdb
TitleCrystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4
Components
  • Arf-GAP with dual PH domain-containing protein 1
  • Kinesin-like protein KIF13B
KeywordsTransport Protein/Hydrolase Activator / KINESIN / GAP / GTPASE ACTIVATION / STRUCTURAL GENOMICS CONSORTIUM / SGC / CYTOSKELETON / MICROTUBULE / MOTOR PROTEIN / ZINC-FINGER / TRANSPORT PROTEIN-HYDROLASE ACTIVATOR COMPLEX / ATP-binding / Nucleotide-binding / Phosphoprotein / Metal-binding / Nucleus
Function / homology
Function and homology information


inositol 1,3,4,5 tetrakisphosphate binding / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / phosphatidylinositol bisphosphate binding / kinesin complex / microtubule motor activity / regulation of axonogenesis / regulation of GTPase activity / microtubule-based movement ...inositol 1,3,4,5 tetrakisphosphate binding / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / phosphatidylinositol bisphosphate binding / kinesin complex / microtubule motor activity / regulation of axonogenesis / regulation of GTPase activity / microtubule-based movement / phosphatidylinositol-3,4,5-trisphosphate binding / protein targeting / Nuclear signaling by ERBB4 / GTPase activator activity / T cell activation / 14-3-3 protein binding / microtubule binding / microtubule / cell surface receptor signaling pathway / axon / intracellular membrane-bounded organelle / protein kinase binding / signal transduction / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADAP, PH domain 1 / ADAP, PH domain 2 / Arf GTPase activating protein / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf ...ADAP, PH domain 1 / ADAP, PH domain 2 / Arf GTPase activating protein / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / ARFGAP/RecO-like zinc finger / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Kinesin-associated / Kinesin-associated / Tumour Suppressor Smad4 - #20 / Annexin V; domain 1 / Tumour Suppressor Smad4 / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-IP9 / Arf-GAP with dual PH domain-containing protein 1 / Kinesin-like protein KIF13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.952 Å
AuthorsShen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4
Authors: Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Kinesin-like protein KIF13B
B: Kinesin-like protein KIF13B
C: Arf-GAP with dual PH domain-containing protein 1
D: Arf-GAP with dual PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,28818
Polymers119,3314
Non-polymers95714
Water0
1
A: Kinesin-like protein KIF13B
C: Arf-GAP with dual PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5579
Polymers59,6652
Non-polymers8927
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF13B
D: Arf-GAP with dual PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7319
Polymers59,6652
Non-polymers657
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.797, 115.797, 189.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Kinesin-like protein KIF13B / / Kinesin-like protein GAKIN


Mass: 13969.805 Da / Num. of mol.: 2 / Fragment: Fha domain (UNP Residues 440 to 545)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF13B, GAKIN, KIAA0639 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9NQT8
#2: Protein Arf-GAP with dual PH domain-containing protein 1 / Centaurin-alpha-1 / Cnt-a1 / Putative MAPK-activating protein PM25


Mass: 45695.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAP1, CENTA1 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O75689
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-IP9 / (2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate / L-a-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl / [(2R)-3-[[(2S,3S,5R,6S)-2,6-dihydroxy-3,4,5-triphosphonooxy-cyclohexyl]oxy-hydroxy-phosphoryl]oxy-2-octanoyloxy-propyl] octanoate


Mass: 826.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H50O22P4
Sequence detailsAUTHORS STATE THAT THEIR SEQUENCE MATCHES NCBI ENTRY NP_006860.1 GI:6806913

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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: 2.66 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Sample buffer: 20mM HEPES, pH 7.30, 500mM NaCl, 1mM TCEP, 5% Glycerol. Protein complex was mixed with PIP3 in 1:1 molar ratio and acetone (5%). Reservoir solution: 0.8M lithium sulfate, 0.5M ...Details: Sample buffer: 20mM HEPES, pH 7.30, 500mM NaCl, 1mM TCEP, 5% Glycerol. Protein complex was mixed with PIP3 in 1:1 molar ratio and acetone (5%). Reservoir solution: 0.8M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Cryo-protectant: 2.0M lithium sulfate., vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97625 Å
DetectorType: MAR300 / Detector: CCD / Date: Oct 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 27800 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.139 / Χ2: 1.302 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0614.70.95727161.1231100
3.06-3.1814.80.69327061.1931100
3.18-3.3214.80.46427541.2241100
3.32-3.514.80.3227261.261100
3.5-3.7214.80.21527411.2551100
3.72-414.70.15827561.3031100
4-4.414.70.11827661.5261100
4.4-5.0414.60.0927961.4961100
5.04-6.3414.40.0828421.2891100
6.34-3013.60.04529971.3441100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: nearly isomorphous coordinates of PDB entry 3FM8

3fm8


Resolution: 2.952→29.437 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.205 / SU B: 18.738 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The programs PHENIX and COOT and the PRODRG and MOLPRPOBITY servers were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 978 3.526 %thin shells
Rwork0.225 ---
obs0.227 27736 99.964 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.609 Å20 Å20 Å2
2--0.609 Å20 Å2
3----1.218 Å2
Refinement stepCycle: LAST / Resolution: 2.952→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7066 0 41 0 7107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0217291
X-RAY DIFFRACTIONr_bond_other_d0.0010.024891
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9429911
X-RAY DIFFRACTIONr_angle_other_deg0.806311802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6723.265343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.777151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5591547
X-RAY DIFFRACTIONr_chiral_restr0.0680.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021592
X-RAY DIFFRACTIONr_mcbond_it1.13624540
X-RAY DIFFRACTIONr_mcbond_other0.14321823
X-RAY DIFFRACTIONr_mcangle_it1.99437203
X-RAY DIFFRACTIONr_scbond_it0.8622751
X-RAY DIFFRACTIONr_scangle_it1.42132708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.952-3.0280.419490.3021937199599.549
3.028-3.110.3871120.2691811192499.948
3.11-3.19900.2619091909100
3.199-3.2970.3231010.25617491850100
3.297-3.4030.342780.24917141792100
3.403-3.5210.294230.23717131736100
3.521-3.6520.313670.22116041671100
3.652-3.7990.28780.21315151593100
3.799-3.9650.255680.20615091577100
3.965-4.1540.196560.18414341490100
4.154-4.3740.245570.1813581415100
4.374-4.63300.1813831383100
4.633-4.9440.239360.18312231259100
4.944-5.3280.23760.20711311207100
5.328-5.8170.278390.2210801119100
5.817-6.4730.329290.2729841013100
6.473-7.4140.393220.257900922100
7.414-8.940.276330.217764797100
8.94-12.0970.203300.235614644100
12.097-29.4370.278240.316426450100

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