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- PDB-3bch: Crystal Structure of the Human Laminin Receptor Precursor -

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Basic information

Entry
Database: PDB / ID: 3bch
TitleCrystal Structure of the Human Laminin Receptor Precursor
Components40S ribosomal protein SA
KeywordsCELL ADHESION / RIBOSOMAL PROTEIN / laminin receptor / p40 ribosomal protein / Acetylation / Cytoplasm / Phosphorylation / Polymorphism / Ribonucleoprotein
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency ...Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / laminin binding / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / virus receptor activity / cytoplasmic translation / SARS-CoV-2 modulates host translation machinery / structural constituent of ribosome / translation / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glucose-6-phosphate isomerase like protein; domain 1 / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 ...Glucose-6-phosphate isomerase like protein; domain 1 / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJamieson, K.V. / Wu, J. / Hubbard, S.R. / Meruelo, D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of the human laminin receptor precursor.
Authors: Jamieson, K.V. / Wu, J. / Hubbard, S.R. / Meruelo, D.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 40S ribosomal protein SA


Theoretical massNumber of molelcules
Total (without water)28,2051
Polymers28,2051
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.688, 75.688, 99.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 40S ribosomal protein SA / / p40 / 34/67 kDa laminin receptor / Colon carcinoma laminin-binding protein / NEM/1CHD4 / Multidrug ...p40 / 34/67 kDa laminin receptor / Colon carcinoma laminin-binding protein / NEM/1CHD4 / Multidrug resistance- associated protein MGr1-Ag


Mass: 28205.045 Da / Num. of mol.: 1 / Fragment: laminin receptor precursor (UNP residues 2-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPSA, LAMBR, LAMR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08865
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 18989 / Num. obs: 18989
Reflection shellResolution: 2.15→2.15 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.743 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22396 820 5.1 %RANDOM
Rwork0.18536 ---
obs0.18718 15415 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 147 1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221599
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9542173
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4465196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10822.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17915269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5161515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.2687
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21094
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.51016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16121591
X-RAY DIFFRACTIONr_scbond_it1.6263673
X-RAY DIFFRACTIONr_scangle_it2.824.5582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 69 -
Rwork0.19 1086 -
obs--99.74 %

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