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- PDB-3g2s: VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide -

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Basic information

Entry
Database: PDB / ID: 3g2s
TitleVHS Domain of human GGA1 complexed with SorLA C-terminal Peptide
Components
  • ADP-ribosylation factor-binding protein GGA1
  • 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 / adaptive thermogenesis / post-Golgi vesicle-mediated transport ...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 / adaptive thermogenesis / post-Golgi vesicle-mediated transport / protein retention in Golgi apparatus / protein transporter activity / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / positive regulation of protein exit from endoplasmic reticulum / low-density lipoprotein particle receptor activity / negative regulation of amyloid precursor protein catabolic process / endosome to plasma membrane protein transport / low-density lipoprotein particle binding / Golgi to plasma membrane transport / aspartic-type endopeptidase inhibitor activity / Golgi to plasma membrane protein transport / protein targeting to lysosome / multivesicular body membrane / neuropeptide binding / regulation of smooth muscle cell migration / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / insulin receptor recycling / transport vesicle membrane / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / negative regulation of BMP signaling pathway / neuropeptide signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / protein targeting / positive regulation of adipose tissue development / multivesicular body / phosphatidylinositol binding / receptor-mediated endocytosis / ubiquitin binding / intracellular protein transport / trans-Golgi network / protein catabolic process / recycling endosome / small GTPase binding / negative regulation of neurogenesis / recycling endosome membrane / positive regulation of protein catabolic process / transmembrane signaling receptor activity / intracellular protein localization / cell migration / amyloid-beta binding / early endosome membrane / early endosome / endosome / endosome membrane / Amyloid fiber formation / Golgi membrane / neuronal cell body / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / Golgi apparatus / 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 / 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 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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 / Fibronectin type III domain / EGF-like domain signature 2. / 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
HEXANE-1,6-DIOL / Sortilin-related receptor / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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


Theoretical massNumber of molelcules
Total (without water)36,7645
Polymers36,6464
Non-polymers1181
Water4,954275
1
A: ADP-ribosylation factor-binding protein GGA1
C: C-terminal fragment of Sortilin-related receptor


Theoretical massNumber of molelcules
Total (without water)18,3232
Polymers18,3232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-5 kcal/mol
Surface area9000 Å2
MethodPISA
2
B: ADP-ribosylation factor-binding protein GGA1
D: C-terminal fragment of Sortilin-related receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4413
Polymers18,3232
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-4 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.430, 52.890, 136.350
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-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: 1364.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q92673
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2007
RadiationMonochromator: high resolution Si(311) cut and a lower resolution Si(111) cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 34624 / Num. obs: 34575 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.21 % / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 8.26 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.81 / Num. unique all: 5312 / % possible all: 99.7

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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: 1.7→49.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU B: 4.283 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / ESU R: 0.119 / ESU R Free: 0.113 / Phase error: 20.12 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1728 5 %RANDOM
Rwork0.196 32838 --
obs0.197 34566 99.84 %-
all-34624 --
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: 43.098 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 101.7 Å2 / Biso mean: 19.96 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.467 Å2-0 Å20 Å2
2---0.551 Å20 Å2
3---0.084 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 8 275 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092565
X-RAY DIFFRACTIONf_angle_d1.2243469
X-RAY DIFFRACTIONf_chiral_restr0.095391
X-RAY DIFFRACTIONf_plane_restr0.018443
X-RAY DIFFRACTIONf_dihedral_angle_d18.866994
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.2661400.23526622802100
1.75-1.8060.2711400.22226652805100
1.806-1.8710.2311430.2127102853100
1.871-1.9460.2321430.21127192862100
1.946-2.0350.2451430.19327232866100
2.035-2.1420.2461420.18626892831100
2.142-2.2760.2141430.19327292872100
2.276-2.4520.2381430.18327152858100
2.452-2.6980.2211450.19727522897100
2.698-3.0890.241460.20427632909100
3.089-3.8910.2021460.18227872933100
3.891-49.3310.1861540.182924307899
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)
10.9921-0.0796-0.90571.3826-0.06151.4631-0.10670.1219-0.0712-0.0439-0.0178-0.01650.102-0.06920.08710.0631-0.02080.00380.0808-0.02330.069912.3843-10.9475-25.5608
21.17950.2545-0.7162.98080.0511.22840.0546-0.00730.01810.2829-0.03570.15650.00720.0013-0.00090.08840.00180.0180.096-0.01760.06255.93787.3497-9.861
30.2878-0.298-0.43271.9141-0.253-0.38520.07140.2230.0972-0.4611-0.0130.00330.16040.0576-0.06390.1689-0.0241-0.01880.17670.03070.107215.79363.0211-37.2976
40.0364-0.0374-0.18250.3760.2269-0.1467-0.0662-0.23340.18060.15340.0301-0.1022-0.26560.2719-0.12970.13120.02240.00290.27340.00480.106420.651912.4015-13.4341
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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