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- PDB-1j2j: Crystal structure of GGA1 GAT N-terminal region in complex with A... -

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Basic information

Entry
Database: PDB / ID: 1j2j
TitleCrystal structure of GGA1 GAT N-terminal region in complex with ARF1 GTP form
Components(ADP-ribosylation factor ...) x 2
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


Glycosphingolipid transport / synaptic vesicle budding / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Golgi to transport vesicle transport / lysosomal membrane organization / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic ...Glycosphingolipid transport / synaptic vesicle budding / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Golgi to transport vesicle transport / lysosomal membrane organization / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / protein localization to ciliary membrane / mitotic cleavage furrow ingression / positive regulation of ER to Golgi vesicle-mediated transport / Lysosome Vesicle Biogenesis / COPI-mediated anterograde transport / very-low-density lipoprotein particle assembly / regulation of receptor internalization / Synthesis of PIPs at the plasma membrane / regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of calcium ion-dependent exocytosis / COPI-dependent Golgi-to-ER retrograde traffic / postsynaptic actin cytoskeleton organization / Golgi Associated Vesicle Biogenesis / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / MHC class II antigen presentation / dendritic spine organization / retrograde transport, endosome to Golgi / protein localization to cell surface / long-term synaptic depression / TBC/RABGAPs / positive regulation of sodium ion transmembrane transport / positive regulation of dendritic spine development / cell leading edge / positive regulation of endocytosis / intracellular copper ion homeostasis / endomembrane system / vesicle-mediated transport / sarcomere / phosphatidylinositol binding / small monomeric GTPase / ubiquitin binding / actin filament organization / positive regulation of protein secretion / intracellular protein transport / trans-Golgi network / protein catabolic process / cellular response to virus / small GTPase binding / positive regulation of protein catabolic process / GDP binding / protein localization / protein transport / late endosome / early endosome membrane / postsynaptic density / early endosome / endosome membrane / neuron projection / Amyloid fiber formation / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / magnesium ion binding / protein-containing complex / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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. / ADP-ribosylation factor 1-5 / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Small GTPase superfamily, ARF type / Clathrin adaptor, appendage, Ig-like subdomain superfamily / small GTPase Arf family profile. / ENTH/VHS / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / ARF-like small GTPases; ARF, ADP-ribosylation factor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / IODIDE ION / ADP-ribosylation factor 1 / ADP-ribosylation factor 2 / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
Authors: Shiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
History
DepositionJan 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
B: ADP-ribosylation factor binding protein GGA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1216
Polymers24,3202
Non-polymers8014
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-21 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.410, 61.894, 76.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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ADP-ribosylation factor ... , 2 types, 2 molecules AB

#1: Protein ADP-ribosylation factor 1 / ARF1


Mass: 18951.615 Da / Num. of mol.: 1 / Fragment: residues 18-181 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pProEX HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8BSL7, UniProt: P84078*PLUS
#2: Protein/peptide ADP-ribosylation factor binding protein GGA1


Mass: 5368.233 Da / Num. of mol.: 1 / Fragment: GAT N-terminal region
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 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UJY5

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Non-polymers , 4 types, 282 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.13 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350, KI, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 %PEG33501reservoir
20.2 M1reservoirKI
35 mM1dropMgCl2
410 mMTris-HCl1droppH8.0
530 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2002
RadiationMonochromator: Si (111) + Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 30626 / Num. obs: 30625 / % possible obs: 96.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3 / % possible all: 83.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 30626 / Num. measured all: 194166
Reflection shell
*PLUS
% possible obs: 83.1 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J2I

1j2i
PDB Unreleased entry


Resolution: 1.6→24.85 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.752 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22701 1545 5 %RANDOM
Rwork0.19848 ---
all0.19988 ---
obs0.19988 29080 100 %-
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: 16.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 35 278 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211722
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9832327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0363204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10915327
X-RAY DIFFRACTIONr_chiral_restr0.1080.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021272
X-RAY DIFFRACTIONr_nbd_refined0.2130.3810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.5234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.524
X-RAY DIFFRACTIONr_mcbond_it0.8711.51022
X-RAY DIFFRACTIONr_mcangle_it1.61221641
X-RAY DIFFRACTIONr_scbond_it2.5713700
X-RAY DIFFRACTIONr_scangle_it4.2834.5686
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 85
Rwork0.266 1681
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.56

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