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- PDB-4aow: Crystal structure of the human Rack1 protein at a resolution of 2... -

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Basic information

Entry
Database: PDB / ID: 4aow
TitleCrystal structure of the human Rack1 protein at a resolution of 2.45 angstrom
ComponentsGUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
KeywordsRECEPTOR / WD-REPEAT / BETA-PROPELLER
Function / homology
Function and homology information


negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of peptidyl-serine phosphorylation / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide ...negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of peptidyl-serine phosphorylation / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / pigmentation / ion channel inhibitor activity / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / negative regulation of translational frameshifting / BH3 domain binding / regulation of cell division / phagocytic cup / positive regulation of intrinsic apoptotic signaling pathway / translation regulator activity / signaling adaptor activity / gastrulation / rescue of stalled ribosome / negative regulation of protein binding / positive regulation of GTPase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / cyclin binding / enzyme activator activity / protein kinase C binding / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of smoothened signaling pathway / positive regulation of protein-containing complex assembly / Regulation of TNFR1 signaling / cellular response to glucose stimulus / negative regulation of cell growth / cellular response to growth factor stimulus / receptor tyrosine kinase binding / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / positive regulation of protein phosphorylation / ribosome binding / small ribosomal subunit / midbody / cytosolic small ribosomal subunit / protein phosphatase binding / molecular adaptor activity / perikaryon / cytoplasmic translation / regulation of cell cycle / negative regulation of translation / protein ubiquitination / positive regulation of cell migration / cadherin binding / positive regulation of apoptotic process / signaling receptor binding / negative regulation of gene expression / neuronal cell body / dendrite / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Small (40S) ribosomal subunit Asc1/RACK1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Small (40S) ribosomal subunit Asc1/RACK1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRuiz Carrillo, D. / Chandrasekaran, R. / Nilsson, M. / Cornvick, T. / Liew, C.W. / Tan, S.M. / Lescar, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Human Rack1 Protein at a Resolution of 2.45 A.
Authors: Ruiz Carrillo, D. / Chandrasekaran, R. / Nilsson, M. / Cornvik, T. / Liew, C.W. / Tan, S.M. / Lescar, J.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
B: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
C: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6015
Polymers113,4173
Non-polymers1842
Water3,333185
1
A: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1


Theoretical massNumber of molelcules
Total (without water)37,8061
Polymers37,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9903
Polymers37,8061
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1


Theoretical massNumber of molelcules
Total (without water)37,8061
Polymers37,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.260, 134.260, 135.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.006525, 0.4445, -0.8957), (-0.01206, -0.8957, -0.4444), (-0.9999, 0.007906, 0.01121)30.48, -165.1, -18.13
2given(-0.008033, 0.9007, 0.4344), (-0.03739, 0.4339, -0.9002), (-0.9993, -0.02347, 0.03019)98.49, -38.09, 12

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Components

#1: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 / RECEPTOR FOR ACTIVATED C KINASE 1 / CELL PROLIFERATION-INDUCI GUANINE NUCLEOTIDE-BINDING PROTEIN ...RECEPTOR FOR ACTIVATED C KINASE 1 / CELL PROLIFERATION-INDUCI GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN 12.3 / HUMAN LUNG CANCER ONCOGENE 7 PROTEIN / HLC-7 / RECEPTOR FOR ACTIVATED C KINASE / RECEPTOR OF ACTIVATED PROTEIN KINASE C 1 / RACK1


Mass: 37805.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA T1R / References: UniProt: P63244
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.69 Å3/Da / Density % sol: 54.36 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→47.63 Å / Num. obs: 45262 / % possible obs: 98.8 % / Observed criterion σ(I): 2.5 / Redundancy: 9.3 % / Biso Wilson estimate: 50.28 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.4
Reflection shellResolution: 2.45→2.59 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.5 / % possible all: 92.1

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DM0

3dm0


Resolution: 2.45→35.87 Å / Cor.coef. Fo:Fc: 0.9078 / Cor.coef. Fo:Fc free: 0.8901 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 2280 5.05 %RANDOM
Rwork0.193 ---
obs0.1941 45179 --
Displacement parametersBiso mean: 45.84 Å2
Baniso -1Baniso -2Baniso -3
1-3.1308 Å20 Å20 Å2
2--3.1308 Å20 Å2
3----6.2616 Å2
Refine analyzeLuzzati coordinate error obs: 0.327 Å
Refinement stepCycle: LAST / Resolution: 2.45→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 12 185 7172
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017132HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.189721HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2344SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1043HARMONIC5
X-RAY DIFFRACTIONt_it7132HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion19.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion956SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7929SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2357 139 5.4 %
Rwork0.2196 2436 -
all0.2205 2575 -
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)
12.5337-0.3098-0.24260.9262-0.07732.38690.0378-0.17380.20450.1216-0.0111-0.0101-0.6245-0.0244-0.02670.35820.0115-0.02660.1307-0.01830.0612-2.687-53.415-7.174
21.1164-0.2368-0.09141.0266-0.00392.58080.0446-0.0182-0.0455-0.0091-0.00470.1196-0.0729-0.2705-0.03990.2118-0.0143-0.02470.2383-0.01960.0494-9.192-70.125-4.808
32.3850.3123-0.44471.5074-0.20181.87920.09760.1022-0.7523-0.00510.03230.05980.2237-0.1549-0.12980.0993-0.0466-0.07220.1689-0.07080.4334-11.9561-114.254-19.6841
42.85710.2734-0.7362.5155-0.03281.06710.1622-0.3392-0.38230.2235-0.07260.1415-0.0763-0.0233-0.08960.1287-0.0786-0.04620.26610.02830.2236-14.5671-102.113-6.6533
52.95510.1618-0.47692.20810.53951.94290.17370.33070.2048-0.1567-0.19010.2217-0.031-0.13940.01650.11680.1091-0.0480.29820.01860.291821.223-97.377-30.062
63.21670.2053-0.0181.16480.29281.33750.1765-0.1601-0.44870.0053-0.20140.11450.1998-0.02320.02480.13960.013-0.0710.2832-0.03270.375319.29-110.854-18.7753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3-141
2X-RAY DIFFRACTION2CHAIN A AND RESID 142-314
3X-RAY DIFFRACTION3CHAIN B AND RESID 3-141
4X-RAY DIFFRACTION4CHAIN B AND RESID 142-314
5X-RAY DIFFRACTION5CHAIN C AND RESID 3-146
6X-RAY DIFFRACTION6CHAIN C AND RESID 147-314

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