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- PDB-1ujk: VHS domain of human GGA1 complexed with C-terminal phosphopeptide... -

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Basic information

Entry
Database: PDB / ID: 1ujk
TitleVHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE
Components
  • ADP-ribosylation factor binding protein GGA1
  • C-terminal peptide from Beta-secretase
KeywordsPROTEIN TRANSPORT/Hydrolase / PROTEIN-PEPTIDE COMPLEX / PROTEIN TRANSPORT / ADAPTOR PROTEIN / PROTEIN TRANSPORT-Hydrolase COMPLEX
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 / protein localization to cell surface / TBC/RABGAPs / memapsin 2 / Golgi-associated vesicle lumen / beta-aspartyl-peptidase activity / signaling receptor ligand precursor processing ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / memapsin 2 / Golgi-associated vesicle lumen / beta-aspartyl-peptidase activity / signaling receptor ligand precursor processing / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / cellular response to manganese ion / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / protein serine/threonine kinase binding / presynaptic modulation of chemical synaptic transmission / multivesicular body / phosphatidylinositol binding / hippocampal mossy fiber to CA3 synapse / ubiquitin binding / intracellular protein transport / trans-Golgi network / response to lead ion / protein catabolic process / protein processing / recycling endosome / small GTPase binding / cellular response to amyloid-beta / positive regulation of protein catabolic process / positive regulation of neuron apoptotic process / intracellular protein localization / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / early endosome membrane / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / early endosome / lysosome / endosome / endosome membrane / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / intracellular membrane-bounded organelle / dendrite / enzyme binding / cell surface / Golgi apparatus / protein-containing complex / proteolysis / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / 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 / Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Beta-secretase 1 / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShiba, T. / Kametaka, S. / Kawasaki, M. / Shibata, M. / Waguri, S. / Uchiyama, Y. / Wakatsuki, S.
CitationJournal: TRAFFIC / Year: 2004
Title: Insights into the Phosphoregulation of beta-Secretase Sorting Signal by the VHS Domain of GGA1
Authors: Shiba, T. / Kametaka, S. / Kawasaki, M. / Shibata, M. / Waguri, S. / Uchiyama, Y. / Wakatsuki, S.
History
DepositionAug 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor binding protein GGA1
B: ADP-ribosylation factor binding protein GGA1
C: C-terminal peptide from Beta-secretase
D: C-terminal peptide from Beta-secretase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33110
Polymers36,5704
Non-polymers7616
Water5,206289
1
A: ADP-ribosylation factor binding protein GGA1
C: C-terminal peptide from Beta-secretase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6665
Polymers18,2852
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area8700 Å2
MethodPISA
2
B: ADP-ribosylation factor binding protein GGA1
D: C-terminal peptide from Beta-secretase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6665
Polymers18,2852
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6 kcal/mol
Surface area7940 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-12 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.545, 72.308, 103.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribosylation factor binding protein GGA1 / GGA1


Mass: 16814.436 Da / Num. of mol.: 2 / Fragment: VHS domain, N-terminal domain
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
#2: Protein/peptide C-terminal peptide from Beta-secretase / C-terminal peptide from BACE


Mass: 1470.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized peptide
References: UniProt: P56817, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.39 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 28983 / Num. obs: 28939 / % possible obs: 98.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9→1.97 Å / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWG

1jwg


Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 1451 -RANDOM
Rwork0.2132 ---
all0.2148 28983 --
obs0.2148 28939 98.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 6 289 2705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005376
X-RAY DIFFRACTIONc_angle_deg1.07167

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