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- PDB-1juq: GGA3 VHS domain complexed with C-terminal peptide from cation-dep... -

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Basic information

Entry
Database: PDB / ID: 1juq
TitleGGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor
Components
  • ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
  • Cation-dependent mannose-6-phosphate receptor
KeywordsSIGNALING PROTEIN / protein-peptide complex / VHS domain / dxxll sorting signal
Function / homology
Function and homology information


secretion of lysosomal enzymes / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin-coated vesicle membrane / Golgi to plasma membrane protein transport / protein targeting to lysosome / Golgi to plasma membrane transport / membrane organization / endocytic recycling / MET receptor recycling ...secretion of lysosomal enzymes / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin-coated vesicle membrane / Golgi to plasma membrane protein transport / protein targeting to lysosome / Golgi to plasma membrane transport / membrane organization / endocytic recycling / MET receptor recycling / protein localization to cell surface / TBC/RABGAPs / lysosomal transport / Lysosome Vesicle Biogenesis / endosome to lysosome transport / negative regulation of amyloid-beta formation / plasma membrane => GO:0005886 / transport vesicle / receptor-mediated endocytosis / phosphatidylinositol binding / trans-Golgi network membrane / ubiquitin binding / intracellular protein transport / protein catabolic process / protein destabilization / regulation of protein stability / trans-Golgi network / small GTPase binding / recycling endosome membrane / positive regulation of protein catabolic process / transmembrane signaling receptor activity / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / lysosome / endosome membrane / endosome / Amyloid fiber formation / lysosomal membrane / protein domain specific binding / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / membrane / plasma membrane
Similarity search - Function
GGA3, GAT domain / : / Cation-dependent mannose-6-phosphate receptor / Mannose-6-phosphate receptor / Mannose-6-phosphate receptor / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily ...GGA3, GAT domain / : / Cation-dependent mannose-6-phosphate receptor / Mannose-6-phosphate receptor / Mannose-6-phosphate receptor / 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 / MRH domain profile. / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Mannose-6-phosphate receptor binding domain superfamily / 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 / ENTH/VHS / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cation-dependent mannose-6-phosphate receptor / ADP-ribosylation factor-binding protein GGA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD/FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMisra, S. / Puertollano, R. / Bonifacino, J.S. / Hurley, J.H.
CitationJournal: Nature / Year: 2002
Title: Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains.
Authors: Misra, S. / Puertollano, R. / Kato, Y. / Bonifacino, J.S. / Hurley, J.H.
History
DepositionAug 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 12, 2016Group: Advisory
Remark 300BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The authors have gel filtration and analytical ultracentrifugation data that suggest that the asymmetric unit contains 4 biological units (chains A/E, B/F, C/G, D/H). The authors think the apparent dimer in the crystal is due to crystallization.

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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 GGA3
E: Cation-dependent mannose-6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-dependent mannose-6-phosphate receptor
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-dependent mannose-6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)85,2748
Polymers85,2748
Non-polymers00
Water3,153175
1
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,3192
Polymers21,3192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-6 kcal/mol
Surface area8620 Å2
MethodPISA
2
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,3192
Polymers21,3192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area8880 Å2
MethodPISA
3
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,3192
Polymers21,3192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,3192
Polymers21,3192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-7 kcal/mol
Surface area9180 Å2
MethodPISA
5
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-dependent mannose-6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-dependent mannose-6-phosphate receptor

B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-dependent mannose-6-phosphate receptor
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)85,2748
Polymers85,2748
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
Buried area8240 Å2
ΔGint-49 kcal/mol
Surface area30310 Å2
MethodPISA
6
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-dependent mannose-6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3

B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-dependent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)82,0716
Polymers82,0716
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
Buried area6310 Å2
ΔGint-34 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.640, 131.350, 108.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3


Mass: 19716.924 Da / Num. of mol.: 4 / Fragment: VHS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGA3 / Plasmid: pHis-parallel2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZ52
#2: Protein/peptide
Cation-dependent mannose-6-phosphate receptor /


Mass: 1601.691 Da / Num. of mol.: 4 / Fragment: C-terminal peptide / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P20645
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
PH range low: 11 / PH range high: 10.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
21.5 mMpeptide1drop
3100 mMCAPS1reservoirpH10.2-11.0
4200 mM1reservoirLi2SO4
51.33-2 Msodium potassium phospahte1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONNSLS X9B20.97900,0.97946,0.96859
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJun 23, 2001mirrors
ADSC QUANTUM 42CCDJun 3, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteSINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9791
30.979461
40.968591
ReflectionResolution: 2.2→100 Å / Num. obs: 43908 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Redundancy: 3.57 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.97 / Num. unique all: 3823 / % possible all: 86.7
Reflection shell
*PLUS
% possible obs: 86.7 % / Num. unique obs: 3823 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD/FOURIER SYNTHESIS / Resolution: 2.2→90.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 628452.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4269 10.1 %RANDOM
Rwork0.221 ---
obs-42356 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3598 Å2 / ksol: 0.385002 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.89 Å20 Å20 Å2
2--13.22 Å20 Å2
3----7.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→90.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 0 175 5389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 597 9.9 %
Rwork0.255 5439 -
obs--81.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 90 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.255 / Rfactor obs: 0.258

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