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- PDB-1dvp: CRYSTAL STRUCTURE OF THE VHS AND FYVE TANDEM DOMAINS OF HRS, A PR... -

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Basic information

Entry
Database: PDB / ID: 1dvp
TitleCRYSTAL STRUCTURE OF THE VHS AND FYVE TANDEM DOMAINS OF HRS, A PROTEIN INVOLVED IN MEMBRANE TRAFFICKING AND SIGNAL TRANSDUCTION
ComponentsHEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
KeywordsTRANSFERASE / HRS / VHS / FYVE / Zinc finger / superhelix
Function / homology
Function and homology information


negative regulation of torso signaling pathway / Lysosome Vesicle Biogenesis / RHOBTB3 ATPase cycle / regulation of epithelial cell migration, open tracheal system / Endosomal Sorting Complex Required For Transport (ESCRT) / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / positive regulation of Toll signaling pathway / Clathrin-mediated endocytosis / Ub-specific processing proteases ...negative regulation of torso signaling pathway / Lysosome Vesicle Biogenesis / RHOBTB3 ATPase cycle / regulation of epithelial cell migration, open tracheal system / Endosomal Sorting Complex Required For Transport (ESCRT) / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / positive regulation of Toll signaling pathway / Clathrin-mediated endocytosis / Ub-specific processing proteases / positive regulation of Wnt protein secretion / positive regulation of border follicle cell migration / exosomal secretion / endosome transport via multivesicular body sorting pathway / early endosome to late endosome transport / endocytic recycling / endosomal transport / neuron remodeling / negative regulation of smoothened signaling pathway / ubiquitin binding / intracellular protein transport / receptor internalization / endocytosis / cell cortex / regulation of cell cycle / endosome / perinuclear region of cytoplasm / metal ion binding / cytosol
Similarity search - Function
Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Zinc finger, FYVE/PHD-type / Alpha Horseshoe / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Hepatocyte growth factor-regulated tyrosine kinase substrate
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMao, Y. / Nickitenko, A. / Duan, X. / Lloyd, T.E. / Wu, M.N. / Bellen, H. / Quiocho, F.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction.
Authors: Mao, Y. / Nickitenko, A. / Duan, X. / Lloyd, T.E. / Wu, M.N. / Bellen, H. / Quiocho, F.A.
History
DepositionJan 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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

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Assembly

Deposited unit
A: HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4394
Polymers25,1161
Non-polymers3233
Water4,270237
1
A: HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
hetero molecules

A: HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8788
Polymers50,2322
Non-polymers6466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)116.706, 69.665, 41.799
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE / HRS


Mass: 25115.869 Da / Num. of mol.: 1 / Fragment: N-TERMINAL VHS AND FYVE TANDEM DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q960X8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG10000, Sodium Citrate, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 mMdithiothreitol1drop
350 mMcitrate1drop
415 %PEG100001reservoir
55 mMdithiothreitol1reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9717
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 22957 / Num. obs: 22397 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.29 / Num. unique all: 2261 / % possible all: 100
Reflection
*PLUS
Num. obs: 22957 / Num. measured all: 89859
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2075 -RANDOM
Rwork0.215 ---
all0.227 22068 --
obs0.219 20914 92.4 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 15 237 1980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.6

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