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- PDB-3tjz: Crystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex -

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Basic information

Entry
Database: PDB / ID: 3tjz
TitleCrystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex
Components
  • ADP-ribosylation factor 1
  • Coatomer subunit gamma
  • Coatomer subunit zeta-1
Keywordsprotein transport/protein binding / protein trafficking / Golgi membrane / protein transport-protein binding complex
Function / homology
Function and homology information


Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / COPI-dependent Golgi-to-ER retrograde traffic / regulation of Golgi organization / COPI-mediated anterograde transport / organelle membrane contact site ...Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / COPI-dependent Golgi-to-ER retrograde traffic / regulation of Golgi organization / COPI-mediated anterograde transport / organelle membrane contact site / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / Golgi vesicle transport / organelle transport along microtubule / positive regulation of mitochondrial fusion / regulation of fatty acid metabolic process / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of mitochondrial fission / endoplasmic reticulum-Golgi intermediate compartment / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / small monomeric GTPase / intracellular protein transport / macroautophagy / Golgi membrane / GTPase activity / GTP binding / structural molecule activity / endoplasmic reticulum / Golgi apparatus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal / Coatomer, gamma subunit, appendage domain superfamily / Coatomer subunit zeta / Coatomer gamma subunit appendage platform subdomain / Coatomer subunit gamma-1 C-terminal appendage platform / Beta-Lactamase - #60 / ADP-ribosylation factor 1-5 / Clathrin adaptor complex, small chain ...Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal / Coatomer, gamma subunit, appendage domain superfamily / Coatomer subunit zeta / Coatomer gamma subunit appendage platform subdomain / Coatomer subunit gamma-1 C-terminal appendage platform / Beta-Lactamase - #60 / ADP-ribosylation factor 1-5 / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Beta-Lactamase / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Alpha Horseshoe / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor 1 / Coatomer subunit zeta-1 / Coatomer subunit gamma-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsGoldberg, J. / Yu, X. / Breitman, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: A structure-based mechanism for arf1-dependent recruitment of coatomer to membranes.
Authors: Yu, X. / Breitman, M. / Goldberg, J.
History
DepositionAug 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Coatomer subunit gamma
C: Coatomer subunit zeta-1
D: ADP-ribosylation factor 1
E: Coatomer subunit gamma
F: Coatomer subunit zeta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,13410
Polymers151,0416
Non-polymers1,0934
Water00
1
A: ADP-ribosylation factor 1
B: Coatomer subunit gamma
C: Coatomer subunit zeta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0675
Polymers75,5213
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-41 kcal/mol
Surface area25090 Å2
MethodPISA
2
D: ADP-ribosylation factor 1
E: Coatomer subunit gamma
F: Coatomer subunit zeta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0675
Polymers75,5213
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-40 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.579, 163.579, 145.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ADP-ribosylation factor 1


Mass: 18665.225 Da / Num. of mol.: 2 / Fragment: unp residues 18-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARF1, YDL192W, D1244 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P11076
#2: Protein Coatomer subunit gamma / Gamma-coat protein / Gamma-COP


Mass: 39375.480 Da / Num. of mol.: 2 / Fragment: unp residues 1-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: COPG / Plasmid: pFastBac / Cell line (production host): Hi-5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53620
#3: Protein Coatomer subunit zeta-1 / Zeta-1-coat protein / Zeta-1 COP


Mass: 17479.992 Da / Num. of mol.: 2 / Fragment: unp residues 1-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: COPZ1, COPZ / Plasmid: pFastBac1 / Cell line (production host): Hi-5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35604
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.22 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG 400, 0.1 M MES-NaOH pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. all: 83327 / Num. obs: 83327 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→45 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 3782 4.54 %
Rwork0.2062 --
obs0.2087 83278 99.88 %
all-83278 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.642 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.433 Å20 Å20 Å2
2--1.433 Å2-0 Å2
3----2.866 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 66 0 8970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099125
X-RAY DIFFRACTIONf_angle_d1.28512340
X-RAY DIFFRACTIONf_dihedral_angle_d17.723402
X-RAY DIFFRACTIONf_chiral_restr0.091425
X-RAY DIFFRACTIONf_plane_restr0.0051547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9005-2.93720.39251390.31232890X-RAY DIFFRACTION98
2.9372-2.97580.40351330.27242963X-RAY DIFFRACTION100
2.9758-3.01660.35151420.28352887X-RAY DIFFRACTION100
3.0166-3.05970.38641400.25232962X-RAY DIFFRACTION100
3.0597-3.10530.28621420.23612954X-RAY DIFFRACTION100
3.1053-3.15390.27261410.21472946X-RAY DIFFRACTION100
3.1539-3.20550.29891390.22052977X-RAY DIFFRACTION100
3.2055-3.26080.33391400.2272932X-RAY DIFFRACTION100
3.2608-3.32010.31721340.22562954X-RAY DIFFRACTION100
3.3201-3.38390.32691430.22512934X-RAY DIFFRACTION100
3.3839-3.4530.31781430.22962942X-RAY DIFFRACTION100
3.453-3.52810.27621410.20832953X-RAY DIFFRACTION100
3.5281-3.61010.25311420.20352945X-RAY DIFFRACTION100
3.6101-3.70030.26711400.20282942X-RAY DIFFRACTION100
3.7003-3.80040.24351420.18192961X-RAY DIFFRACTION100
3.8004-3.91210.22561400.18422941X-RAY DIFFRACTION100
3.9121-4.03840.28081410.1952942X-RAY DIFFRACTION100
4.0384-4.18260.31531380.19772949X-RAY DIFFRACTION100
4.1826-4.350.21651410.17382948X-RAY DIFFRACTION100
4.35-4.54780.21241430.16012956X-RAY DIFFRACTION100
4.5478-4.78740.24131420.16182936X-RAY DIFFRACTION100
4.7874-5.0870.1921390.17762952X-RAY DIFFRACTION100
5.087-5.47930.27671430.19792952X-RAY DIFFRACTION100
5.4793-6.02980.29121370.23952945X-RAY DIFFRACTION100
6.0298-6.90030.27471360.23722954X-RAY DIFFRACTION100
6.9003-8.68560.20431370.18672943X-RAY DIFFRACTION100
8.6856-48.73470.22051440.23052936X-RAY DIFFRACTION99

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