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- PDB-3zyq: Crystal structure of the tandem VHS and FYVE domains of Hepatocyt... -

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Entry
Database: PDB / ID: 3zyq
TitleCrystal structure of the tandem VHS and FYVE domains of Hepatocyte growth factor-regulated tyrosine kinase substrate (HGS-Hrs) at 1.48 A resolution
ComponentsHEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
KeywordsSIGNALING
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 / positive regulation of exosomal secretion / RHOBTB3 ATPase cycle / protein targeting to lysosome / 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 / positive regulation of exosomal secretion / RHOBTB3 ATPase cycle / protein targeting to lysosome / negative regulation of receptor signaling pathway via JAK-STAT / membrane fission / multivesicular body assembly / multivesicular body membrane / endocytic recycling / protein localization to membrane / negative regulation of platelet-derived growth factor receptor signaling pathway / endosomal transport / Lysosome Vesicle Biogenesis / 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) / InlB-mediated entry of Listeria monocytogenes into host cell / phosphatidylinositol binding / negative regulation of angiogenesis / EGFR downregulation / ubiquitin binding / Negative regulation of MET activity / macroautophagy / receptor internalization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / early endosome / lysosome / Ub-specific processing proteases / endosome / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular exosome / zinc 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 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 ...Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / 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. / 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 / Zinc finger, FYVE/PHD-type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor-regulated tyrosine kinase substrate
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMuniz, J.R.C. / Ayinampudi, V. / Shrestha, L. / Krojer, T. / Vollmar, M. / 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) at 1.48 A Resolution
Authors: Muniz, J.R.C. / Ayinampudi, V. / Shrestha, L. / Krojer, T. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bullock, A.
History
DepositionAug 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 / 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.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)26,3996
Polymers26,0481
Non-polymers3515
Water2,792155
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.256, 34.346, 170.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE / HRS / PROTEIN PP110


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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O14964
#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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.15 Å3/Da / Density % sol: 42.81 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97695
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97695 Å / Relative weight: 1
ReflectionResolution: 1.48→42.63 Å / Num. obs: 36946 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→85.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.876 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1843 5 %RANDOM
Rwork0.16444 ---
obs0.16693 35011 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.15 Å2
2--0.68 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.48→85.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 15 155 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221883
X-RAY DIFFRACTIONr_bond_other_d0.0010.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.952551
X-RAY DIFFRACTIONr_angle_other_deg0.9533226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99824.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51915353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8031515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
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_restr3.20133205
X-RAY DIFFRACTIONr_sphericity_free29.8075101
X-RAY DIFFRACTIONr_sphericity_bonded12.3953217
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 142 -
Rwork0.28 2438 -
obs--96.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66710.03140.44590.9340.21971.72580.0422-0.0399-0.19780.00570.0160.00780.1423-0.0292-0.05810.0913-0.0058-0.00450.08260.00110.1035-2.423812.387-23.9961
22.95360.30851.04881.08430.16772.2040.0786-0.2459-0.35110.08290.01110.03120.3038-0.1915-0.08970.113-0.0020.00330.15410.00560.1093-6.851413.7242-8.9083
31.1558-0.08711.21870.3295-0.58253.0063-0.0597-0.14140.13020.05280.0028-0.0353-0.2508-0.12190.05690.15430.028-0.00460.1969-0.02090.168-12.259723.8335-11.1599
41.89570.34740.53211.59570.66952.3961-0.0012-0.0990.01650.0807-0.0097-0.00160.0066-0.02850.01090.06010.00730.0040.0540.01120.093-29.967228.684-35.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 83
2X-RAY DIFFRACTION2A84 - 117
3X-RAY DIFFRACTION3A118 - 157
4X-RAY DIFFRACTION4A158 - 222

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