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- PDB-3g2v: VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosph... -

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Basic information

Entry
Database: PDB / ID: 3g2v
TitleVHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide
Components
  • ADP-ribosylation factor-binding protein GGA1
  • C-terminal fragment of Sortilin
KeywordsPROTEIN TRANSPORT / ADP-ribosylation factor binding protein GGA1 / VHS / acidic-cluster dileucine signal / Sortilin
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / protein localization to ciliary membrane / Golgi to lysosome transport / plasma membrane to endosome transport / myotube differentiation / nerve growth factor receptor activity / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / retromer complex binding / Golgi to endosome transport ...neurotensin receptor activity, non-G protein-coupled / protein localization to ciliary membrane / Golgi to lysosome transport / plasma membrane to endosome transport / myotube differentiation / nerve growth factor receptor activity / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / retromer complex binding / Golgi to endosome transport / endosome transport via multivesicular body sorting pathway / nerve growth factor binding / vesicle organization / protein targeting to lysosome / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / TBC/RABGAPs / protein localization to cell surface / clathrin-coated vesicle / Golgi cisterna membrane / endosome to lysosome transport / Golgi Associated Vesicle Biogenesis / negative regulation of fat cell differentiation / neurotrophin TRK receptor signaling pathway / D-glucose import / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / phosphatidylinositol binding / ossification / ubiquitin binding / intracellular protein transport / protein catabolic process / trans-Golgi network / response to insulin / small GTPase binding / endocytosis / positive regulation of protein catabolic process / intracellular protein localization / regulation of gene expression / cytoplasmic vesicle / early endosome membrane / nuclear membrane / early endosome / lysosome / endosome membrane / G protein-coupled receptor signaling pathway / Amyloid fiber formation / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / protein-containing complex / 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. / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal ...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. / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / : / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Sortilin / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCramer, J.F. / Behrens, M.A. / Gustafsen, C. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S.
CitationJournal: Traffic / Year: 2010
Title: GGA autoinhibition revisited
Authors: Cramer, J.F. / Gustafsen, C. / Behrens, M.A. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S.
History
DepositionFeb 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 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 16, 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
C: C-terminal fragment of Sortilin
B: ADP-ribosylation factor-binding protein GGA1
D: C-terminal fragment of Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7029
Polymers37,0684
Non-polymers6355
Water2,756153
1
A: ADP-ribosylation factor-binding protein GGA1
C: C-terminal fragment of Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9155
Polymers18,5342
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area8010 Å2
MethodPISA
2
B: ADP-ribosylation factor-binding protein GGA1
D: C-terminal fragment of Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7884
Polymers18,5342
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-3 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.000, 72.900, 102.500
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 / Golgi-localized / gamma ear-containing / ARF-binding protein 1 / Gamma-adaptin-related protein 1


Mass: 16958.564 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-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: UniProt: Q9UJY5
#2: Protein/peptide C-terminal fragment of Sortilin / neurotensin receptor 3 / NTS3 / NTR3 / NT3


Mass: 1575.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q99523
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 16%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 3, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→43.5 Å / Num. all: 21651 / Num. obs: 21642 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.92 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8.13 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.44 / Num. unique all: 2767 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JWF

1jwf


Resolution: 2.1→43.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.846 / SU B: 8.964 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2.01 / ESU R: 0.215 / ESU R Free: 0.192 / Phase error: 22.06 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1081 5 %RANDOM
Rwork0.204 20555 --
obs0.206 21636 99.95 %-
all-21651 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.857 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 128.01 Å2 / Biso mean: 39.744 Å2 / Biso min: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1-6.292 Å2-0 Å2-0 Å2
2---1.333 Å2-0 Å2
3----6.222 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 5 153 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012435
X-RAY DIFFRACTIONf_angle_d1.0833282
X-RAY DIFFRACTIONf_chiral_restr0.093366
X-RAY DIFFRACTIONf_plane_restr0.011418
X-RAY DIFFRACTIONf_dihedral_angle_d21.69932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.1960.2491320.21325142646
2.196-2.3110.2581320.20125112643
2.311-2.4560.2381330.20125312664
2.456-2.6460.271350.20725522687
2.646-2.9120.2411340.21825542688
2.912-3.3330.2491350.22125682703
3.333-4.1990.2291370.18126032740
4.199-43.4790.2241430.19927222865
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.06420.73370.04352.1844-0.11321.93510.1019-0.07480.0246-0.0104-0.21580.1289-0.1789-0.01520.12140.06060.0077-0.0010.27540.00240.20778.3888-9.347-4.2942
21.62140.24890.7411.5301-0.28536.1543-0.10720.07440.021-0.17190.10530.11410.0691-0.0113-0.00740.19640.02210.03980.19580.0740.2437.3207-1.5953-28.8138
30.25820.2425-0.18250.2475-0.13670.13510.12470.3424-0.1909-0.1275-0.14081.3551-0.3416-0.6048-0.19440.32250.0438-0.09180.5189-0.07740.5326-8.152-13.6475-6.9545
42.58672.10872.52361.5916-1.80021.42050.2295-0.3983-0.3151-0.5845-0.50640.05361.22-0.58760.3880.5041-0.1170.02320.48310.16960.57821.3447-17.2937-30.4173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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