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- PDB-4bkw: Crystal structure of the C-terminal region of human ZFYVE9 -

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Basic information

Entry
Database: PDB / ID: 4bkw
TitleCrystal structure of the C-terminal region of human ZFYVE9
ComponentsZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9
KeywordsRECEPTOR / PROTEIN INTERACTION DOMAIN / TGF-BETA AND EGFR SIGNALLING / SGC
Function / homology
Function and homology information


1-phosphatidylinositol binding / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endosomal transport / TGF-beta receptor signaling activates SMADs / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / liver development / endocytosis / early endosome membrane ...1-phosphatidylinositol binding / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endosomal transport / TGF-beta receptor signaling activates SMADs / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / liver development / endocytosis / early endosome membrane / early endosome / protein domain specific binding / intracellular membrane-bounded organelle / protein-containing complex / metal ion binding / cytosol
Similarity search - Function
Domain of unknown function (DUF3480), N-terminal subdomain / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #40 / Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) ...Domain of unknown function (DUF3480), N-terminal subdomain / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #40 / Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / 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. / Gyrase A; domain 2 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger FYVE domain-containing protein 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å
AuthorsWilliams, E. / Krojer, T. / Vollmar, M. / Shrestha, L. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Ph D Thesis / Year: 2013
Title: Crystal Structure of the C-Terminal Region of Human Zfyve9
Authors: Williams, E.
History
DepositionApr 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Assembly

Deposited unit
A: ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7737
Polymers59,2691
Non-polymers5056
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.751, 113.751, 155.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9 / MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG-INTERACTING PROTEIN / MADH-INTERACTING PROTEIN / NOVEL ...MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG-INTERACTING PROTEIN / MADH-INTERACTING PROTEIN / NOVEL SERINE PROTEASE / NSP / RECEPTOR ACTIVATION ANCHOR / HSARA / SMAD ANCHOR FOR RECEPTOR ACTIVATION / ZFYVE9C


Mass: 59268.820 Da / Num. of mol.: 1 / Fragment: PROTEIN INTERACTING DOMAIN, RESIDUES 895-1425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MGM / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O95405
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M BIS-TRIS PH 6.5, 0.15M MAGNESIUM CHLORIDE, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.53→19.99 Å / Num. obs: 20314 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 63.45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
CCP4phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.53→19.7 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.8958 / SU R Cruickshank DPI: 0.438 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.459 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.269
Details: DISORDERED REGIONS WERE LEFT UN- MODELED. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1037 5.1 %RANDOM
Rwork0.2035 ---
obs0.2056 20314 99.76 %-
Displacement parametersBiso mean: 50.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.5282 Å20 Å20 Å2
2--0.5282 Å20 Å2
3----1.0565 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: LAST / Resolution: 2.53→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 33 52 3773
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095143HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1283SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes543HARMONIC5
X-RAY DIFFRACTIONt_it3800HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion18.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion503SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4057SEMIHARMONIC4
LS refinement shellResolution: 2.53→2.67 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2982 156 5.41 %
Rwork0.2394 2729 -
all0.2425 2885 -
obs--99.76 %

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