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- PDB-2yw8: Crystal structure of human RUN and FYVE domain-containing protein -

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Basic information

Entry
Database: PDB / ID: 2yw8
TitleCrystal structure of human RUN and FYVE domain-containing protein
ComponentsRUN and FYVE domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / STRUCTURE GENOMICS / FYVE domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


small GTPase-mediated signal transduction / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / SH2 domain binding / SH3 domain binding / endocytosis / protein transport / early endosome membrane / endosome / nuclear speck ...small GTPase-mediated signal transduction / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / SH2 domain binding / SH3 domain binding / endocytosis / protein transport / early endosome membrane / endosome / nuclear speck / intracellular membrane-bounded organelle / lipid binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / FYVE zinc finger / FYVE zinc finger ...: / : / : / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RUN and FYVE domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, H. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of human RUN and FYVE domain-containing protein
Authors: Wang, H. / Kishishita, S. / Murayama, T. / Takemoto, C. / Terada, T. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: RUN and FYVE domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5744
Polymers9,3471
Non-polymers2273
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.150, 115.150, 115.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein RUN and FYVE domain-containing protein 1 / FYVE-finger protein EIP1 / Zinc finger FYVE domain-containing protein 12 / La-binding protein 1 / ...FYVE-finger protein EIP1 / Zinc finger FYVE domain-containing protein 12 / La-binding protein 1 / Rab4-interacting protein / MS1309 protein


Mass: 9346.705 Da / Num. of mol.: 1 / Fragment: UNP residues 627-708
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: RUFY1, RABIP4, ZFYVE12 / Plasmid: PK060327-08 / References: UniProt: Q96T51
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 6.8 Å3/Da / Density % sol: 81.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis-tris, Ammonium sulfate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.2752 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2752 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 5650 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 40.9 % / Rsym value: 0.153 / Net I/σ(I): 30.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 42.5 % / Mean I/σ(I) obs: 12.5 / Num. unique all: 544 / Rsym value: 0.414 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VFY

1vfy


Resolution: 3→47.01 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 44214.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 314 5.6 %RANDOM
Rwork0.198 ---
obs0.198 5593 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.5452 Å2 / ksol: 0.356852 e/Å3
Displacement parametersBiso mean: 50.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms487 0 7 34 528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 53 6 %
Rwork0.26 832 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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