[English] 日本語
Yorodumi
- PDB-3f1i: Human ESCRT-0 Core Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f1i
TitleHuman ESCRT-0 Core Complex
Components
  • Hepatocyte growth factor-regulated tyrosine kinase substrate
  • Signal transducing adapter molecule 1
KeywordsPROTEIN BINDING / HGS / STAM / ESCRT / ubiquitin / MVB / Endosome / Membrane / Metal-binding / Phosphoprotein / Protein transport / Transport / Zinc-finger / SH3 domain
Function / homology
Function and homology information


Inhibition of membrane repair / ESCRT-0 complex / membrane invagination / regulation of extracellular exosome assembly / 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 ...Inhibition of membrane repair / ESCRT-0 complex / membrane invagination / regulation of extracellular exosome assembly / 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 / protein localization to membrane / endocytic recycling / 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) / negative regulation of angiogenesis / phosphatidylinositol binding / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / macroautophagy / EGFR downregulation / Negative regulation of MET activity / receptor internalization / Metalloprotease DUBs / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / lysosome / early endosome / Ub-specific processing proteases / endosome / negative regulation of cell population proliferation / protein domain specific binding / intracellular membrane-bounded organelle / positive regulation of gene expression / signal transduction / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1940 / STAM1, SH3 domain / : / : / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1940 / STAM1, SH3 domain / : / : / 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. / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 domain / Zinc finger, FYVE/PHD-type / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Hepatocyte growth factor-regulated tyrosine kinase substrate / Signal transducing adapter molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsRen, X. / Kloer, D.P. / Kim, Y. / Ghirlando, R. / Saidi, L. / Hummer, G. / Hurley, J.H.
CitationJournal: Structure / Year: 2009
Title: Hybrid Structural Model of the Complete Human ESCRT-0 Complex.
Authors: Ren, X. / Kloer, D.P. / Kim, Y.C. / Ghirlando, R. / Saidi, L.F. / Hummer, G. / Hurley, J.H.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Hepatocyte growth factor-regulated tyrosine kinase substrate
S: Signal transducing adapter molecule 1
C: Signal transducing adapter molecule 1


Theoretical massNumber of molelcules
Total (without water)29,3243
Polymers29,3243
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-42 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.059, 78.059, 152.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Hepatocyte growth factor-regulated tyrosine kinase substrate / Protein pp110 / Hrs


Mass: 11393.910 Da / Num. of mol.: 1 / Fragment: Helical domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: Hepatocyte growth factor regulated tyrosine kinase substrate (HGS), HGS, HRS
Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLys / References: UniProt: O14964
#2: Protein Signal transducing adapter molecule 1 / STAM-1


Mass: 8965.172 Da / Num. of mol.: 2 / Fragment: Helical domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: Signal transducing adaptor molecule (STAM), STAM, STAM1
Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLys / References: UniProt: Q92783
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% MPD, 100 mM CaCl2, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jun 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→69.5 Å / Num. obs: 20041 / Redundancy: 7.5 % / Rsym value: 0.077 / Net I/σ(I): 23.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.325

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→44.77 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.815 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25305 1019 5.1 %RANDOM
Rwork0.23871 ---
obs0.23941 19005 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.794 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--1.29 Å20 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 28 1642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211632
X-RAY DIFFRACTIONr_bond_other_d0.0010.021135
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9892188
X-RAY DIFFRACTIONr_angle_other_deg0.93832782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9745196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91925.39389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13615331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9441513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_nbd_refined0.2120.2371
X-RAY DIFFRACTIONr_nbd_other0.1630.21047
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2770
X-RAY DIFFRACTIONr_nbtor_other0.0860.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.51316
X-RAY DIFFRACTIONr_mcbond_other0.1731.5395
X-RAY DIFFRACTIONr_mcangle_it121590
X-RAY DIFFRACTIONr_scbond_it2.1323699
X-RAY DIFFRACTIONr_scangle_it3.0984.5598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 75 -
Rwork0.233 1301 -
obs--93.04 %
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)
11.2553-0.2475-0.08391.66750.23731.3544-0.0006-0.04050.12970.03510.00060.0865-0.1442-0.1265-0.00010.4824-0.0079-0.00070.49350.00240.480911.721-1.23070.296
27.177-1.9763-3.32529.41139.463116.50890.3659-0.93660.3484-0.21780.376-0.81260.4641.1166-0.7418-0.26570.04120.0305-0.0271-0.0316-0.171938.2404-10.885-5.0933
330.7832-17.4329-17.638110.229.93910.2831-0.3867-1.0008-0.20550.27120.47730.1060.26311.1018-0.0906-0.21880.06370.02630.06790.0611-0.21524.0695-5.881210.5153
454.5088-12.1305-7.85098.04651.55064.55220.30960.26390.3136-0.3388-0.37350.5712-0.4477-1.11980.0639-0.16910.0696-0.06370.0688-0.0947-0.2158-18.188610.378519.5209
525.9874-4.7085-7.43954.07231.65936.91060.3557-0.20581.52270.1512-0.0253-0.4217-0.4603-0.0974-0.3304-0.1120.00080.0029-0.2547-0.0905-0.0999-3.852411.889125.7938
631.5938-26.9837-22.640925.945721.673618.27341.08940.80321.3192-0.9176-0.5902-0.6129-1.187-0.3699-0.4992-0.0691-0.00090.0981-0.15620.1557-0.03778.68569.823212.5348
714.1657-10.6381-6.107417.92019.142813.9081-0.3599-0.3643-1.23970.1580.33610.56412.0241-0.17760.02380.1068-0.00030.0501-0.09020.0844-0.164131.2233-18.466-3.2425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C64 - 90
2X-RAY DIFFRACTION2H404 - 439
3X-RAY DIFFRACTION3H440 - 472
4X-RAY DIFFRACTION4H473 - 501
5X-RAY DIFFRACTION5S301 - 324
6X-RAY DIFFRACTION6S325 - 359
7X-RAY DIFFRACTION7S360 - 377

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more