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- PDB-3g2u: VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide -

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Basic information

Entry
Database: PDB / ID: 3g2u
TitleVHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide
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 / protein localization to cell surface / TBC/RABGAPs / 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: 2.301 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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 30, 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: C-terminal fragment of Sortilin
D: C-terminal fragment of Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5439
Polymers36,9084
Non-polymers6355
Water2,648147
1
A: ADP-ribosylation factor-binding protein GGA1
C: C-terminal fragment of Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9626
Polymers18,4542
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-2 kcal/mol
Surface area7760 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)18,5813
Polymers18,4542
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.486, 72.728, 103.767
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: 1495.438 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.: 147 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15%(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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2007
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.3→43.5 Å / Num. all: 16852 / Num. obs: 16683 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.66 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2428 / % possible all: 99.6

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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: 2.301→37.601 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.836 / SU B: 11.791 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.227 / Phase error: 22.95 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 836 5.03 %RANDOM
Rwork0.199 15793 --
obs0.201 16629 98.4 %-
all-16852 --
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: 36.79 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 135.78 Å2 / Biso mean: 41.418 Å2 / Biso min: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.895 Å20 Å20 Å2
2--0.182 Å20 Å2
3----4.077 Å2
Refinement stepCycle: LAST / Resolution: 2.301→37.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 5 147 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092411
X-RAY DIFFRACTIONf_angle_d0.9863246
X-RAY DIFFRACTIONf_chiral_restr0.081364
X-RAY DIFFRACTIONf_plane_restr0.017414
X-RAY DIFFRACTIONf_dihedral_angle_d22.253922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.4450.2861390.2142586272599
2.445-2.6330.2711480.20826002748100
2.633-2.8980.2621390.2032630276999
2.898-3.3180.2891480.2022612276099
3.318-4.1790.2271310.1792641277298
4.179-37.6060.1961310.1962724285596
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)
12.18021.0719-0.27952.09740.29743.3020.0704-0.10230.1384-0.0399-0.16150.096-0.2038-0.0882-0.03310.04460.0156-0.0170.11170.01230.09457.9323-8.8986-4.4834
21.21460.62730.87561.98420.00765.633-0.1-0.0711-0.0327-0.13550.04350.1108-0.0863-0.0976-0.00520.11580.02350.02430.05550.07610.14157.7252-1.5753-29.2797
30.53350.2072-0.566-0.2402-0.13680.9070.10090.00150.258-0.130.08590.1949-0.3106-0.48160.03440.2186-0.0513-0.07170.4003-0.07250.2349-6.6136-15.0573-9.7708
40.01050.00690.01550.02550.01850.04290.2251-0.203-0.727-0.2868-0.0976-0.15330.2915-0.6735-00.4939-0.20740.0360.57280.28280.72480.582-16.7458-30.1765
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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