[English] 日本語
Yorodumi
- PDB-1naf: Crystal structure of the human GGA1 GAT domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1naf
TitleCrystal structure of the human GGA1 GAT domain
ComponentsADP-ribosylation factor binding protein GGA1
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / clathrin-adaptor / GGA / GAT domain / helical paper-clip / three-helix bundle
Function / homology
Function and homology information


protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / TBC/RABGAPs / retrograde transport, endosome to Golgi / protein localization to cell surface / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / trans-Golgi network ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / TBC/RABGAPs / retrograde transport, endosome to Golgi / protein localization to cell surface / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / trans-Golgi network / protein catabolic process / small GTPase binding / positive regulation of protein catabolic process / protein localization / early endosome membrane / early endosome / endosome membrane / Amyloid fiber formation / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / ENTH/VHS / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsCollins, B.M. / Watson, P.J. / Owen, D.J.
CitationJournal: Dev.Cell / Year: 2003
Title: The Structure of the GGA1-GAT Domain Reveals the Molecular Basis for ARF Binding and Membrane Association of GGAs
Authors: Collins, B.M. / Watson, P.J. / Owen, D.J.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Structure summary / Category: exptl_crystal_grow / struct
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _struct.title
Revision 1.4Oct 16, 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: ADP-ribosylation factor binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)18,4121
Polymers18,4121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.700, 82.700, 69.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Cell settinghexagonal
Space group name H-MP63

-
Components

#1: Protein ADP-ribosylation factor binding protein GGA1 / GGA1 appendage domain / Golgi-localized / gamma ear-containing / ARF-binding protein 1 / Gamma- ...GGA1 appendage domain / Golgi-localized / gamma ear-containing / ARF-binding protein 1 / Gamma-adaptin related protein 1


Mass: 18412.449 Da / Num. of mol.: 1 / Fragment: GAT domain, Residues 165-314 of SWS Q9UJY5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9UJY5
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: sodium acetate, lithium sulphate, NaH2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMdithiothreitol1drop
210-15 mg/mlprotein1drop
30.1 Msodium acetate1reservoirpH4.5
40.3 Msodium phosphate1reservoir
50.45 Mpotassium phosphate1reservoir
60.2 M1reservoirLi2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9796, 0.9798, 0.9393
DetectorDetector: CCD / Date: Jun 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.93931
ReflectionResolution: 2.8→70 Å / Num. obs: 6684 / % possible obs: 99.7 % / Observed criterion σ(F): 2.6 / Redundancy: 3.7 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2833 294 random
Rwork0.2483 --
all0.2485 6768 -
obs0.2484 5495 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.609 Å2-29.295 Å20 Å2
2---11.609 Å20 Å2
3---23.219 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 0 0 1006
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.18

+
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