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- PDB-3g2t: VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphop... -

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Basic information

Entry
Database: PDB / ID: 3g2t
TitleVHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide
Components
  • ADP-ribosylation factor-binding protein GGA1
  • Phosphorylated C-terminal fragment of Sortilin-related receptor
KeywordsPROTEIN TRANSPORT / ADP-ribosylation factor binding protein GGA1 / VHS / acidic-cluster dileucine signal / SorLA
Function / homology
Function and homology information


positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / protein localization to ciliary membrane / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / post-Golgi vesicle-mediated transport / adaptive thermogenesis ...positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / protein localization to ciliary membrane / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / post-Golgi vesicle-mediated transport / adaptive thermogenesis / protein retention in Golgi apparatus / low-density lipoprotein particle receptor activity / endosome to plasma membrane protein transport / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / low-density lipoprotein particle binding / positive regulation of protein exit from endoplasmic reticulum / negative regulation of amyloid precursor protein catabolic process / Golgi to plasma membrane transport / protein targeting to lysosome / Golgi to plasma membrane protein transport / aspartic-type endopeptidase inhibitor activity / multivesicular body membrane / neuropeptide binding / regulation of smooth muscle cell migration / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / transport vesicle membrane / insulin receptor recycling / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / protein maturation / negative regulation of BMP signaling pathway / neuropeptide signaling pathway / protein targeting / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / positive regulation of adipose tissue development / multivesicular body / phosphatidylinositol binding / receptor-mediated endocytosis / ubiquitin binding / intracellular protein transport / protein catabolic process / protein localization / trans-Golgi network / recycling endosome / small GTPase binding / negative regulation of neurogenesis / positive regulation of protein catabolic process / recycling endosome membrane / transmembrane signaling receptor activity / cell migration / amyloid-beta binding / early endosome membrane / early endosome / endosome membrane / endosome / Amyloid fiber formation / Golgi membrane / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum membrane / Golgi apparatus / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / extracellular exosome / 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 / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / GAT domain superfamily / GAT domain / Sortilin, neurotensin receptor 3, C-terminal ...ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / GAT domain superfamily / GAT domain / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / GAT domain profile. / 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 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / ENTH/VHS / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Sortilin-related receptor / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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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: Phosphorylated C-terminal fragment of Sortilin-related receptor
D: Phosphorylated C-terminal fragment of Sortilin-related receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,82112
Polymers36,8064
Non-polymers1,0158
Water5,008278
1
A: ADP-ribosylation factor-binding protein GGA1
C: Phosphorylated C-terminal fragment of Sortilin-related receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1658
Polymers18,4032
Non-polymers7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-5 kcal/mol
Surface area8000 Å2
MethodPISA
2
B: ADP-ribosylation factor-binding protein GGA1
D: Phosphorylated C-terminal fragment of Sortilin-related receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6574
Polymers18,4032
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 68.300, 100.600
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) / References: UniProt: Q9UJY5
#2: Protein/peptide Phosphorylated C-terminal fragment of Sortilin-related receptor / Sorting protein-related receptor containing LDLR class A repeats / SorLA / SorLA-1 / Low-density ...Sorting protein-related receptor containing LDLR class A repeats / SorLA / SorLA-1 / Low-density lipoprotein receptor relative with 11 ligand-binding repeats / LDLR relative with 11 ligand-binding repeats / LR11


Mass: 1444.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q92673
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 26870 / Num. obs: 26556 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.05 % / Biso Wilson estimate: 27.74 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.84
Reflection shellResolution: 2→2.3 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.7 / Num. unique all: 9042 / % 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→40.502 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / FOM work R set: 0.855 / SU B: 7.343 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.4 / ESU R: 0.164 / ESU R Free: 0.16 / Phase error: 21.6 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1327 5 %RANDOM
Rwork0.192 25208 --
obs0.194 26535 99.55 %-
all-26870 --
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: 56.227 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 127.63 Å2 / Biso mean: 36.27 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.347 Å20 Å2-0 Å2
2--3.562 Å2-0 Å2
3----3.909 Å2
Refinement stepCycle: LAST / Resolution: 2→40.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 8 278 2667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082428
X-RAY DIFFRACTIONf_angle_d0.9583277
X-RAY DIFFRACTIONf_chiral_restr0.085369
X-RAY DIFFRACTIONf_plane_restr0.01415
X-RAY DIFFRACTIONf_dihedral_angle_d21.033925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.3331400.2562655279596
2.08-2.1750.291460.2327682914100
2.175-2.2890.2181460.20727772923100
2.289-2.4330.251470.19727852932100
2.433-2.6210.2481460.19527882934100
2.621-2.8840.2291470.19627882935100
2.884-3.3020.2431490.18728252974100
3.302-4.1590.2211490.16328432992100
4.159-40.510.1991570.18629793136100
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)
11.43130.72310.09821.784-0.11721.7638-0.0332-0.0351-0.08750.0755-0.0331-0.07230.25930.10460.00110.14530.0190.02430.16820.02150.122515.71517.50945.1228
22.95261.26120.31182.36880.40093.2701-0.14670.1984-0.3069-0.06990.0486-0.38380.1560.206600.30930.03330.01910.2454-0.02480.299324.1821-4.0512-15.9163
30.60680.6744-0.00390.88541.35140.1560.044-0.4355-0.54940.29170.1127-0.0980.29510.15630.00840.2040.0417-0.00130.29940.06490.298531.412310.71417.1122
40.19460.0435-0.17260.18520.21370.1269-0.29290.70320.0448-0.15550.325-0.26180.197-0.2028-00.3854-0.1027-0.1330.73970.16530.403933.92969.2025-16.2301
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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