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- PDB-1jwg: VHS Domain of human GGA1 complexed with cation-independent M6PR C... -

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Basic information

Entry
Database: PDB / ID: 1jwg
TitleVHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide
Components
  • ADP-ribosylation factor binding protein GGA1
  • Cation-independent mannose-6-phosphate receptor
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / SUPER HELIX / PROTEIN-PEPTIDE COMPLEX / PROTEIN TRANSPORT-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


protein localization to ciliary membrane / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / Golgi to plasma membrane protein transport / Golgi to plasma membrane transport ...protein localization to ciliary membrane / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / Golgi to plasma membrane protein transport / Golgi to plasma membrane transport / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / protein localization to cell surface / retrograde transport, endosome to Golgi / TBC/RABGAPs / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / ubiquitin binding / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / intracellular protein transport / protein catabolic process / trans-Golgi network / protein localization / small GTPase binding / positive regulation of protein catabolic process / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / early endosome membrane / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Amyloid fiber formation / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / GAT domain / GAT domain superfamily / Cation-independent mannose-6-phosphate receptor repeat / GAT domain / GAT domain profile. ...ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / GAT domain / GAT domain superfamily / Cation-independent mannose-6-phosphate receptor repeat / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / MRH domain / 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 / 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
IODIDE ION / Cation-independent mannose-6-phosphate receptor / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShiba, T. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Kawasaki, M. / Igarashi, N. / Suzuki, M. / Kato, R. / Earnest, T. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Nature / Year: 2002
Title: Structural basis for recognition of acidic-cluster dileucine sequence by GGA1.
Authors: Shiba, T. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Kawasaki, M. / Igarashi, N. / Suzuki, M. / Kato, R. / Earnest, T. / Nakayama, K. / Wakatsuki, S.
History
DepositionSep 4, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2002Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Cation-independent mannose-6-phosphate receptor
B: ADP-ribosylation factor binding protein GGA1
D: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,47910
Polymers36,7184
Non-polymers7616
Water3,567198
1
A: ADP-ribosylation factor binding protein GGA1
C: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6134
Polymers18,3592
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylation factor binding protein GGA1
D: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8676
Polymers18,3592
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.146, 65.770, 101.426
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


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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJY5
#2: Protein/peptide Cation-independent mannose-6-phosphate receptor / M6PR


Mass: 1544.577 Da / Num. of mol.: 2 / Fragment: C-terminal fragment / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P11717
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, ammonium iodide, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMTris-HCl1droppH8.0
210 mg/mlprotein1drop
314 %(w/v)PEG33501reservoir
40.2 M1reservoirNH4I
50.1 MTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 24632 / Num. obs: 24632 / % possible obs: 99.6 %
Reflection shellResolution: 2→2.11 Å / % possible all: 99.3
Reflection
*PLUS
Num. obs: 25975 / Num. measured all: 167862 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWF

1jwf


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.933 / SU B: 4.254 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26115 1292 5 %RANDOM
Rwork0.2263 ---
all0.22796 24632 --
obs0.22796 24632 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.099 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--2.78 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 6 198 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9743237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9753288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75615487
X-RAY DIFFRACTIONr_chiral_restr0.0930.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021754
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.31169
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.51458
X-RAY DIFFRACTIONr_mcangle_it1.5422354
X-RAY DIFFRACTIONr_scbond_it2.3263943
X-RAY DIFFRACTIONr_scangle_it3.9764.5883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 83 4.634 %
Rwork0.234 1791 -
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.234

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