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- PDB-4avx: Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (Hgs... -

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Entry
Database: PDB / ID: 4avx
TitleHepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (Hgs-Hrs) bound to an IP2 compound at 1.68 A Resolution
ComponentsHEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
KeywordsSIGNALING PROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / SIGNALING
Function / homology
Function and homology information


Inhibition of membrane repair / ESCRT-0 complex / membrane invagination / regulation of MAP kinase activity / phagocytic vesicle lumen / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to lysosome / RHOBTB3 ATPase cycle / membrane fission / negative regulation of receptor signaling pathway via JAK-STAT ...Inhibition of membrane repair / ESCRT-0 complex / membrane invagination / regulation of MAP kinase activity / phagocytic vesicle lumen / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to lysosome / RHOBTB3 ATPase cycle / membrane fission / negative regulation of receptor signaling pathway via JAK-STAT / multivesicular body membrane / positive regulation of exosomal secretion / multivesicular body assembly / endocytic recycling / protein localization to membrane / negative regulation of platelet-derived growth factor receptor signaling pathway / Lysosome Vesicle Biogenesis / endosomal transport / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of protein catabolic process / ubiquitin-like protein ligase binding / RHOU GTPase cycle / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / negative regulation of angiogenesis / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / EGFR downregulation / macroautophagy / Negative regulation of MET activity / receptor internalization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / lysosome / early endosome / Ub-specific processing proteases / endosome / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular exosome / 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
Chem-ITP / Hepatocyte growth factor-regulated tyrosine kinase substrate
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWilliams, E. / Canning, P. / Shrestha, L. / Krojer, T. / Vollmar, M. / Slowey, A. / Conway, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Williams, E. / Canning, P. / Shrestha, L. / Krojer, T. / Vollmar, M. / Slowey, A. / Conway, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of the Tandem Vhs and Fyve Domains of Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (Hgs-Hrs) Bound to an Ip2 Compound at 1.68 A Resolution
Authors: Williams, E. / Canning, P. / Shrestha, L. / Krojer, T. / Vollmar, M. / Slowey, A. / Conway, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bullock, A.
History
DepositionMay 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,01512
Polymers26,0481
Non-polymers96711
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.825, 67.545, 57.423
Angle α, β, γ (deg.)90.00, 103.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26047.939 Da / Num. of mol.: 1 / Fragment: VHS AND FYVE DOMAINS, RESIDUES 691-915
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O14964
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ITP / PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER / INOSITOL 1,3-BISPHOSPHATE


Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.01 Å3/Da / Density % sol: 38.94 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 5.5; 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→43.03 Å / Num. obs: 22910 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.6
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZYQ

3zyq


Resolution: 1.68→55.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.014 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23103 1167 5.1 %RANDOM
Rwork0.18108 ---
obs0.18357 21700 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.21 Å2
2--0.06 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.68→55.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 54 148 1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021858
X-RAY DIFFRACTIONr_bond_other_d0.0010.021294
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9632500
X-RAY DIFFRACTIONr_angle_other_deg1.0053.0043160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83524.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7921511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02361
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 81 -
Rwork0.263 1520 -
obs--93.03 %
Refinement TLS params.Method: refined / Origin x: 13.516 Å / Origin y: 23.351 Å / Origin z: 8.9623 Å
111213212223313233
T0.0274 Å2-0.0097 Å2-0.0015 Å2-0.0222 Å2-0.0038 Å2--0.0169 Å2
L0.1812 °20.1431 °20.1841 °2-0.2975 °20.2353 °2--0.2539 °2
S-0.0411 Å °-0.0112 Å °-0.0189 Å °-0.0724 Å °0.0399 Å °0.0041 Å °-0.0743 Å °0.008 Å °0.0011 Å °

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