[English] 日本語
Yorodumi
- PDB-2dwy: Crystal Structure Analysis of GGA1-GAE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dwy
TitleCrystal Structure Analysis of GGA1-GAE
ComponentsADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
KeywordsPROTEIN TRANSPORT / IG FOLD / ADAPTIN
Function / homology
Function and homology information


protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / TBC/RABGAPs / protein localization to cell surface / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / TBC/RABGAPs / protein localization to cell surface / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process / trans-Golgi network / small GTPase binding / positive regulation of protein catabolic process / intracellular 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
ADP-ribosylation factor-binding protein GGA3 / Gamma-adaptin ear (GAE) domain / 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 ...ADP-ribosylation factor-binding protein GGA3 / Gamma-adaptin ear (GAE) domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsInoue, M. / Shiba, T. / Yamada, Y. / Ihara, K. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Traffic / Year: 2007
Title: Molecular Basis for Autoregulatory Interaction Between GAE Domain and Hinge Region of GGA1
Authors: Inoue, M. / Shiba, T. / Ihara, K. / Yamada, Y. / Hirano, S. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
History
DepositionAug 21, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)59,5654
Polymers59,5654
Non-polymers00
Water2,666148
1
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)29,7832
Polymers29,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-19 kcal/mol
Surface area12890 Å2
MethodPISA, PQS
6
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1


Theoretical massNumber of molelcules
Total (without water)29,7832
Polymers29,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-18 kcal/mol
Surface area12250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.482, 88.238, 67.224
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1 / GOLGI-LOCALIZED / GAMMA EAR-CONTAINING / ARF-BINDING PROTEIN 1 / GAMMA-ADAPTIN RELATED PROTEIN 1


Mass: 14891.319 Da / Num. of mol.: 4 / Fragment: GAE DOMAIN, RESIDUES 507-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJY5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.38 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24237 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.296 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IU1

1iu1


Resolution: 2.3→41.52 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.891 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1182 5.1 %RANDOM
Rwork0.217 ---
obs0.219 22062 96 %-
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: 44.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å21.01 Å2
2--3.69 Å20 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 0 148 4231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224196
X-RAY DIFFRACTIONr_bond_other_d0.0020.023917
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9715736
X-RAY DIFFRACTIONr_angle_other_deg0.83139156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024526
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02778
X-RAY DIFFRACTIONr_nbd_refined0.2280.2708
X-RAY DIFFRACTIONr_nbd_other0.240.24511
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.22650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9651.52613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79524320
X-RAY DIFFRACTIONr_scbond_it1.72431583
X-RAY DIFFRACTIONr_scangle_it3.0094.51416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 73
Rwork0.304 1390

+
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