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- PDB-3dow: Complex structure of GABA type A receptor associated protein and ... -

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Basic information

Entry
Database: PDB / ID: 3dow
TitleComplex structure of GABA type A receptor associated protein and its binding epitope on calreticulin
Components
  • CRT peptide
  • Gamma-aminobutyric acid receptor-associated protein
KeywordsPROTEIN TRANSPORT / alpha-beta / beta-grasp fold / Cytoplasm / Cytoskeleton / Golgi apparatus / Membrane / Microtubule / Transport / Calcium / Chaperone / Endoplasmic reticulum / Extracellular matrix / Lectin / Metal-binding / Secreted / Zinc
Function / homology
Function and homology information


response to biphenyl / Calnexin/calreticulin cycle / cytolytic granule / nuclear receptor-mediated glucocorticoid signaling pathway / positive regulation of dendritic cell chemotaxis / Assembly of Viral Components at the Budding Site / positive regulation of protein K48-linked ubiquitination / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of trophoblast cell migration / cortical granule ...response to biphenyl / Calnexin/calreticulin cycle / cytolytic granule / nuclear receptor-mediated glucocorticoid signaling pathway / positive regulation of dendritic cell chemotaxis / Assembly of Viral Components at the Budding Site / positive regulation of protein K48-linked ubiquitination / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of trophoblast cell migration / cortical granule / cellular response to electrical stimulus / response to peptide / regulation of meiotic nuclear division / negative regulation of retinoic acid receptor signaling pathway / sequestering of calcium ion / complement component C1q complex binding / endoplasmic reticulum quality control compartment / regulation of Rac protein signal transduction / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / cortical actin cytoskeleton organization / response to glycoside / microtubule associated complex / Scavenging by Class A Receptors / nuclear androgen receptor binding / Scavenging by Class F Receptors / cellular response to lithium ion / Macroautophagy / negative regulation of neuron differentiation / response to testosterone / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / hormone binding / autophagosome membrane / molecular sequestering activity / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome maturation / autophagosome assembly / protein localization to nucleus / protein targeting / beta-tubulin binding / mitophagy / positive regulation of cell cycle / ERAD pathway / sperm midpiece / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / endoplasmic reticulum-Golgi intermediate compartment membrane / peptide binding / acrosomal vesicle / positive regulation of endothelial cell migration / autophagosome / protein export from nucleus / positive regulation of phagocytosis / protein maturation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class I protein complex / positive regulation of non-canonical NF-kappaB signal transduction / MHC class I peptide loading complex / cellular response to virus / GABA-ergic synapse / microtubule cytoskeleton organization / integrin binding / phagocytic vesicle membrane / intracellular calcium ion homeostasis / cellular senescence / unfolded protein binding / nuclear envelope / response to estradiol / protein folding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / protein-folding chaperone binding / ER-Phagosome pathway / carbohydrate binding / cytoplasmic vesicle / spermatogenesis / regulation of apoptotic process / microtubule binding / chemical synaptic transmission / microtubule / lysosome / postsynapse / negative regulation of translation / protein stabilization / ribosome / iron ion binding / endoplasmic reticulum lumen / response to xenobiotic stimulus
Similarity search - Function
Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like ...Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Endoplasmic reticulum targeting sequence. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Concanavalin A-like lectin/glucanase domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Calreticulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThielmann, Y. / Weiergraeber, O.H. / Willbold, D.
CitationJournal: Febs J. / Year: 2009
Title: Structural framework of the GABARAP-calreticulin interface - implications for substrate binding to endoplasmic reticulum chaperones.
Authors: Thielmann, Y. / Weiergraber, O.H. / Mohrluder, J. / Willbold, D.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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: Gamma-aminobutyric acid receptor-associated protein
B: CRT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4833
Polymers15,4182
Non-polymers651
Water52229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5.7 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.043, 97.043, 97.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
DetailsThe predicted biological unit contains one copy of the monomeric GABARAP-CRT peptide complex.

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 14086.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Product contains an N-terminal cloning artifact (glycine-serine) preceding the sequence of native GABARAP.
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O95166
#2: Protein/peptide CRT peptide / Calreticulin / CRP55 / Calregulin / HACBP / ERp60 / grp60


Mass: 1331.407 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide containing amino acids 195-205 of mature calreticulin, CALR_HUMAN, UniProt entry P27797
References: UniProt: P27797
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 27% v/v PEG MME 550, 10 mM ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2007 / Details: Mirrors
RadiationMonochromator: diamond, germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→39.62 Å / Num. all: 6892 / Num. obs: 6892 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.9 / Num. measured all: 6540 / Num. unique all: 985 / Rsym value: 0.399 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KJT

1kjt


Resolution: 2.3→34.31 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 327 -RANDOM
Rwork0.232 ---
all0.233 6892 --
obs0.233 6892 99.7 %-
Displacement parametersBiso max: 75.56 Å2 / Biso mean: 45.275 Å2 / Biso min: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 2 30 1067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_deg0.62
X-RAY DIFFRACTIONf_dihedral_angle_d16.5

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