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- PDB-5cn1: Crystal structure of yeast GGA1_GAE domain-P21 -

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Basic information

Entry
Database: PDB / ID: 5cn1
TitleCrystal structure of yeast GGA1_GAE domain-P21
ComponentsADP-ribosylation factor-binding protein GGA1
KeywordsPROTEIN TRANSPORT / Vesicular transport / GGA1_GAE / accessory protein
Function / homology
Function and homology information


Golgi to endosome transport / Golgi to vacuole transport / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol binding / ubiquitin binding / trans-Golgi network / cytosol
Similarity search - Function
: / 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 ...: / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZhang, F. / Song, Y. / Li, X. / Teng, M.K.
Funding support China, 2items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2012CB917200 and 2009CB825500 China
the Chinese National Natural Science Foundation31270014, 31130018, 30900224 and 10979039 China
CitationJournal: To Be Published
Title: Structural basis for the accessory protein recruitment by yeast GGA1_GAE domain
Authors: Zhang, F. / Song, Y. / Li, X. / Teng, M.K.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)55,1944
Polymers55,1944
Non-polymers00
Water88349
1
A: ADP-ribosylation factor-binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)13,7991
Polymers13,7991
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)13,7991
Polymers13,7991
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)13,7991
Polymers13,7991
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)13,7991
Polymers13,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-13 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.007, 53.585, 71.547
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADP-ribosylation factor-binding protein GGA1 / Golgi-localized / gamma ear-containing / ARF-binding protein 1


Mass: 13798.606 Da / Num. of mol.: 4 / Fragment: GAE domain, UNP residues 433-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GGA1, YDR358W, D9476.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06336
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 1.2 M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21922 / % possible obs: 99.6 % / Redundancy: 4.3 % / Net I/σ(I): 15.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MNM

3mnm


Resolution: 2.31→42.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.711 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26972 1119 5.1 %RANDOM
Rwork0.21235 ---
obs0.21519 20721 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.371 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0 Å2-0.87 Å2
2--1.27 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.31→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 0 49 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193442
X-RAY DIFFRACTIONr_bond_other_d0.0050.023244
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9714670
X-RAY DIFFRACTIONr_angle_other_deg0.8123.0017464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75625.075134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45515589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0091518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.714.0641803
X-RAY DIFFRACTIONr_mcbond_other2.714.0631802
X-RAY DIFFRACTIONr_mcangle_it4.246.0812245
X-RAY DIFFRACTIONr_mcangle_other4.2396.0832246
X-RAY DIFFRACTIONr_scbond_it3.0014.221639
X-RAY DIFFRACTIONr_scbond_other2.9994.221639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6626.2342425
X-RAY DIFFRACTIONr_long_range_B_refined6.68830.5793556
X-RAY DIFFRACTIONr_long_range_B_other6.68230.5893553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 92 -
Rwork0.267 1447 -
obs--96.19 %

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