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- PDB-1lf8: Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 1lf8
TitleComplex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide
Components
  • ADP-ribosylation factor binding protein GGA3
  • Cation-independent mannose-6-phosphate receptor
KeywordsSIGNALING PROTEIN / VHS domain / Protein-phosphopeptide complex
Function / homology
Function and homology information


positive regulation of lysosomal protein catabolic process / clathrin coat / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / response to tetrachloromethane / insulin-like growth factor binding / protein transporter activity / Golgi to plasma membrane transport / insulin-like growth factor II binding / Golgi to plasma membrane protein transport ...positive regulation of lysosomal protein catabolic process / clathrin coat / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / response to tetrachloromethane / insulin-like growth factor binding / protein transporter activity / Golgi to plasma membrane transport / insulin-like growth factor II binding / Golgi to plasma membrane protein transport / trans-Golgi network transport vesicle / protein targeting to lysosome / positive regulation by host of viral process / MET receptor recycling / retinoic acid binding / protein localization to cell surface / TBC/RABGAPs / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / negative regulation of amyloid-beta formation / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / phosphatidylinositol binding / receptor-mediated endocytosis / secretory granule membrane / liver development / ubiquitin binding / post-embryonic development / trans-Golgi network membrane / intracellular protein transport / phosphoprotein binding / trans-Golgi network / clathrin-coated endocytic vesicle membrane / protein catabolic process / protein destabilization / insulin-like growth factor receptor activity / regulation of protein stability / small GTPase binding / recycling endosome membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / early endosome membrane / spermatogenesis / early endosome / lysosome / endosome / endosome membrane / G protein-coupled receptor signaling pathway / positive regulation of apoptotic process / Amyloid fiber formation / Golgi membrane / focal adhesion / Neutrophil degranulation / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
GGA3, GAT domain / : / 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. / Cation-independent mannose-6-phosphate receptor repeat ...GGA3, GAT domain / : / 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. / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / 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 / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / 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 / 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
Cation-independent mannose-6-phosphate receptor / ADP-ribosylation factor-binding protein GGA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsKato, Y. / Misra, S. / Puertollano, R. / Hurley, J.H. / Bonifacino, J.S.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Phosphoregulation of sorting signal-VHS domain interactions by a direct electrostatic mechanism.
Authors: Kato, Y. / Misra, S. / Puertollano, R. / Hurley, J.H. / Bonifacino, J.S.
History
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
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
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 GGA3
B: ADP-ribosylation factor binding protein GGA3
C: ADP-ribosylation factor binding protein GGA3
D: ADP-ribosylation factor binding protein GGA3
E: Cation-independent mannose-6-phosphate receptor
F: Cation-independent mannose-6-phosphate receptor
G: Cation-independent mannose-6-phosphate receptor
H: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)84,0808
Polymers84,0808
Non-polymers00
Water5,405300
1
A: ADP-ribosylation factor binding protein GGA3
E: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,0202
Polymers21,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area8570 Å2
MethodPISA
2
B: ADP-ribosylation factor binding protein GGA3
F: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,0202
Polymers21,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area8900 Å2
MethodPISA
3
C: ADP-ribosylation factor binding protein GGA3
G: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,0202
Polymers21,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area8460 Å2
MethodPISA
4
D: ADP-ribosylation factor binding protein GGA3
H: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)21,0202
Polymers21,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-7 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.540, 129.700, 108.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsEach VHS domain/phosphopeptide complex corresponds to a single biological unit. There are the equivalent of 4 biological complexes per asymmetric unit. The apparent VHS domain dimer is likely a crystallization artifact.

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Components

#1: Protein
ADP-ribosylation factor binding protein GGA3 / Golgi-localized / gamma ear-containing / ARF-binding protein 3


Mass: 19482.451 Da / Num. of mol.: 4 / Fragment: VHS domain (residues 1-166)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHis-parallel2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZ52
#2: Protein/peptide
Cation-independent mannose-6-phosphate receptor / CI MAN-6-P receptor / CI-MPR / Insulin-like growth factor II receptor


Mass: 1537.478 Da / Num. of mol.: 4 / Fragment: C-terminus (residues 2480-2491) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (Human).
References: UniProt: P11717
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1dropNaCl
220 mMTris-HCl1droppH8.0
310 mMdithiothreitol1drop
4100 mMCAPS1reservoirpH10.2-11.0
5200 mM1reservoirLi2SO4
61.4-1.7 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2001 / Details: Osmic Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 37720 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3550 / % possible all: 91.5
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 91.5 % / Rmerge(I) obs: 0.356

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JUQ

1juq


Resolution: 2.3→89.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 713707.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3600 10 %RANDOM
Rwork0.211 ---
all-37720 --
obs-36130 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6607 Å2 / ksol: 0.338167 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2--2.96 Å20 Å2
3----8.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→89.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 0 300 5593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d1.48
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 503 9.7 %
Rwork0.264 4702 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SEP2.PARSEP2.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.48
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / Rfactor Rwork: 0.264

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