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- PDB-1jpl: GGA3 VHS domain complexed with C-terminal peptide from cation-ind... -

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Basic information

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


clathrin coat / positive regulation of lysosomal protein catabolic process / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / protein transporter activity / insulin-like growth factor II binding / protein targeting to lysosome ...clathrin coat / positive regulation of lysosomal protein catabolic process / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / protein transporter activity / insulin-like growth factor II binding / protein targeting to lysosome / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / host-mediated activation of viral process / MET receptor recycling / retinoic acid binding / endocytic recycling / Golgi to plasma membrane protein transport / TBC/RABGAPs / protein localization to cell surface / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / negative regulation of amyloid-beta formation / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / phosphatidylinositol binding / receptor-mediated endocytosis / secretory granule membrane / trans-Golgi network membrane / ubiquitin binding / post-embryonic development / intracellular protein transport / phosphoprotein binding / protein catabolic process / trans-Golgi network / clathrin-coated endocytic vesicle membrane / liver development / protein destabilization / regulation of protein stability / small GTPase binding / recycling endosome membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / early endosome membrane / spermatogenesis / early endosome / lysosome / endosome / endosome membrane / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Amyloid fiber formation / Golgi membrane / focal adhesion / Neutrophil degranulation / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
GGA3, GAT domain / : / 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. / Cation-independent mannose-6-phosphate receptor repeat ...GGA3, GAT domain / : / 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. / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / 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 / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH 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 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor / ADP-ribosylation factor-binding protein GGA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 2, 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)84,6988
Polymers84,6988
Non-polymers00
Water4,270237
1
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,1742
Polymers21,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-5 kcal/mol
Surface area9010 Å2
MethodPISA
2
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,1742
Polymers21,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5 kcal/mol
Surface area8890 Å2
MethodPISA
3
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,1742
Polymers21,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-6 kcal/mol
Surface area9090 Å2
MethodPISA
4
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,1742
Polymers21,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area9050 Å2
MethodPISA
5
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor

C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)84,6988
Polymers84,6988
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_647-x+3/2,y-1/2,-z+21
Buried area10380 Å2
ΔGint-48 kcal/mol
Surface area29980 Å2
MethodPISA
6
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor

C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)84,6988
Polymers84,6988
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9780 Å2
ΔGint-46 kcal/mol
Surface area30570 Å2
MethodPISA
7
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor

C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)84,6988
Polymers84,6988
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_457x-1/2,-y+1/2,-z+21
Buried area9280 Å2
ΔGint-45 kcal/mol
Surface area31070 Å2
MethodPISA
8
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor

C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)84,6988
Polymers84,6988
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+1,-y+1,z-11
Buried area9250 Å2
ΔGint-44 kcal/mol
Surface area31100 Å2
MethodPISA
9
C: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
G: Cation-Independent Mannose 6-phosphate receptor
D: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
H: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)42,3494
Polymers42,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-22 kcal/mol
Surface area15890 Å2
MethodPISA
10
A: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
E: Cation-Independent Mannose 6-phosphate receptor
B: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
F: Cation-Independent Mannose 6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)42,3494
Polymers42,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-21 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.300, 125.300, 64.600
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 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-Independent Mannose 6-phosphate receptor


Mass: 1457.499 Da / Num. of mol.: 4 / Fragment: C-terminal peptide / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P11717
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.6
Details: 1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97900, 0.97938, 0.95369
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2001
RadiationMonochromator: Focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979381
30.953691
ReflectionResolution: 2.4→99 Å / Num. all: 34965 / Num. obs: 34790 / % possible obs: 99.5 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 10.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 26.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 6.7 / Num. unique all: 3381 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 99.3 % / Num. unique obs: 3381

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Processing

Software
NameVersionClassification
SOLVEphasing
RESOLVEmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→35.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 253695.9 / 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
Rfree0.257 6184 10 %RANDOM
Rwork0.213 ---
all-62036 --
obs-62036 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.8533 Å2 / ksol: 0.371704 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.29 Å20 Å20 Å2
2--3.11 Å20 Å2
3---5.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 0 237 5655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 914 9.8 %
Rwork0.263 8388 -
obs-9302 84.5 %
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: 2.4 Å / Lowest resolution: 35 Å / % reflection Rfree: 10 % / Rfactor obs: 0.214 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.311 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.263 / Rfactor obs: 0.262

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