[English] 日本語
Yorodumi
- PDB-3fhn: Structure of Tip20p -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fhn
TitleStructure of Tip20p
ComponentsProtein transport protein TIP20
KeywordsTRANSPORT PROTEIN / Tip20p / vesicle tethering / Endoplasmic reticulum / ER-Golgi transport / Membrane / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information


Dsl1/NZR complex / COPI-dependent Golgi-to-ER retrograde traffic / regulation of ER to Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagy / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum / cytosol
Similarity search - Function
Dsl1p vesicle tethering complex, Tip20p subunit, domain E / Dsl1p vesicle tethering complex, Tip20p subunit, domain C / Dsl1p vesicle tethering complex, Tip20p subunit, domain B / Dsl1p vesicle tethering complex, Tip20p subunit, domain A / Dsl1p vesicle tethering complex, Tip20p subunit, domain D / RINT-1/Tip20 / Protein transport protein Tip20, domain E / Protein transport protein Tip20, domain A / Protein transport protein Tip20, domain B / Protein transport protein Tip20, domain C ...Dsl1p vesicle tethering complex, Tip20p subunit, domain E / Dsl1p vesicle tethering complex, Tip20p subunit, domain C / Dsl1p vesicle tethering complex, Tip20p subunit, domain B / Dsl1p vesicle tethering complex, Tip20p subunit, domain A / Dsl1p vesicle tethering complex, Tip20p subunit, domain D / RINT-1/Tip20 / Protein transport protein Tip20, domain E / Protein transport protein Tip20, domain A / Protein transport protein Tip20, domain B / Protein transport protein Tip20, domain C / RINT-1/TIP-1 family / RINT1/TIP20 domain profile. / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Tetracycline Repressor; domain 2 / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein transport protein TIP20
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsTripathi, A. / Ren, Y. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural characterization of Tip20p and Dsl1p, subunits of the Dsl1p vesicle tethering complex.
Authors: Tripathi, A. / Ren, Y. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein transport protein TIP20
B: Protein transport protein TIP20
C: Protein transport protein TIP20
D: Protein transport protein TIP20


Theoretical massNumber of molelcules
Total (without water)328,8774
Polymers328,8774
Non-polymers00
Water00
1
A: Protein transport protein TIP20


Theoretical massNumber of molelcules
Total (without water)82,2191
Polymers82,2191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein transport protein TIP20


Theoretical massNumber of molelcules
Total (without water)82,2191
Polymers82,2191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein transport protein TIP20


Theoretical massNumber of molelcules
Total (without water)82,2191
Polymers82,2191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein transport protein TIP20


Theoretical massNumber of molelcules
Total (without water)82,2191
Polymers82,2191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.480, 111.620, 149.840
Angle α, β, γ (deg.)77.09, 88.12, 70.35
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Protein transport protein TIP20


Mass: 82219.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIP20, TIP1, YGL145W / Production host: Escherichia coli (E. coli) / References: UniProt: P33891
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3:1 ratio of protein (2 mg ml-1) and well buffer (0.1 M ADA, pH 6.0, 10% (w/v) PEG monomethyl ether 5K, 0.2 M LiSO4, 3% (v/v) isopropanol, 5 mM DTT), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792, 0.9794, 0.9640
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2007
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.9641
ReflectionResolution: 3→50 Å / Num. all: 99867 / Num. obs: 99867 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.077
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.497 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→29.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1760823.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 5002 5 %RANDOM
Rwork0.22 ---
obs0.22 99867 98.2 %-
all-99867 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.3525 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 81 Å2
Baniso -1Baniso -2Baniso -3
1--3.5 Å2-9.9 Å22.47 Å2
2--7.99 Å28.03 Å2
3----4.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22040 0 0 0 22040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 821 5 %
Rwork0.329 15753 -
obs--97.6 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

+
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://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