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- PDB-1py1: Complex of GGA1-VHS domain and beta-secretase C-terminal phosphop... -

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Basic information

Entry
Database: PDB / ID: 1py1
TitleComplex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide
Components
  • ADP-ribosylation factor binding protein GGA1
  • Beta-secretase
KeywordsPROTEIN TRANSPORT / VHS DOMAIN OF GGA1 / BETA-SECRETASE / PROTEIN-PEPTIDE COMPLEX / SUPER HELIX
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 / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity ...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 / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / 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 / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / multivesicular body / hippocampal mossy fiber to CA3 synapse / phosphatidylinositol binding / ubiquitin binding / response to lead ion / intracellular protein transport / trans-Golgi network / protein catabolic process / recycling endosome / protein processing / small GTPase binding / positive regulation of protein catabolic process / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / 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 membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / 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
Beta-secretase 1 / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhu, G. / Zhang, X.C.
CitationJournal: Biochemistry / Year: 2003
Title: Biochemical and structural characterization of the interaction of memapsin 2 (beta-secretase) cytosolic domain with the VHS domain of GGA proteins.
Authors: He, X. / Zhu, G. / Koelsch, G. / Rodgers, K. / Zhang, X.C. / Tang, J.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
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
Revision 1.4Nov 6, 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: ADP-ribosylation factor binding protein GGA1
D: ADP-ribosylation factor binding protein GGA1
E: Beta-secretase
F: Beta-secretase
G: Beta-secretase
H: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)75,6548
Polymers75,6548
Non-polymers00
Water66737
1
A: ADP-ribosylation factor binding protein GGA1
B: ADP-ribosylation factor binding protein GGA1
E: Beta-secretase
F: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)37,8274
Polymers37,8274
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ADP-ribosylation factor binding protein GGA1
D: ADP-ribosylation factor binding protein GGA1
G: Beta-secretase
H: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)37,8274
Polymers37,8274
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.140, 95.420, 107.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 17958.586 Da / Num. of mol.: 4 / Fragment: VHS Domain (Residues 2-157)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGA1 / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJY5
#2: Protein/peptide
Beta-secretase / Beta-site APP cleaving enzyme / Beta-site amyloid precursor protein cleaving enzyme / Aspartyl ...Beta-site APP cleaving enzyme / Beta-site amyloid precursor protein cleaving enzyme / Aspartyl protease 2 / Asp 2 / ASP2 / Membrane-associated aspartic protease 2 / Memapsin-2


Mass: 954.979 Da / Num. of mol.: 4 / Fragment: C-TERMINUS (RESIDUES 494-501) / Source method: obtained synthetically / Details: YES
References: UniProt: P56817, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 48.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 3350, AMMONIUM SULFATE, CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG33501reservoir
20.2 Mammonium sulfate1reservoir
30.1 Msodium cacodylate1reservoirpH6.4
40.1 %(v/v)beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2003
RadiationMonochromator: OSMIC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 22869 / Num. obs: 22025 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.8
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 4 / Num. unique all: 2229 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 22869 / % possible obs: 99.5 %
Reflection shell
*PLUS
% possible obs: 98.9 % / Num. unique obs: 2229 / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWG

1jwg


Resolution: 2.6→39.45 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 858 3.9 %RANDOM
Rwork0.236 ---
all0.24 22869 --
obs0.236 22006 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.6879 Å2 / ksol: 0.307058 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.5 Å20 Å20 Å2
2--15.37 Å20 Å2
3----19.87 Å2
Refine analyzeLuzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.53 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 0 37 4776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.511 67 3.4 %
Rwork0.392 1883 -
obs--86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4SEP.PAR
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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