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- PDB-5tqb: Crystal structure of assembly chaperone of ribosomal protein L4 (... -

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Basic information

Entry
Database: PDB / ID: 5tqb
TitleCrystal structure of assembly chaperone of ribosomal protein L4 (Acl4) in complex with ribosomal protein L4 (RpL4)
Components
  • 60S ribosomal protein L4-like proteinRibosome
  • Assembly chaperone of ribosomal protein L4 (Acl4)
KeywordsRIBOSOMAL PROTEIN / Ribosome Assembly Chaperone
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
Tetratricopeptide repeat / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L4, eukaryotic and archaeal type / TPR repeat profile. / Ribosomal protein L1e signature. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily ...Tetratricopeptide repeat / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L4, eukaryotic and archaeal type / TPR repeat profile. / Ribosomal protein L1e signature. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein / 60S ribosomal protein L4-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHuber, F.M. / Hoelz, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Heritage Medical Research Institute United States
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis for protection of ribosomal protein L4 from cellular degradation.
Authors: Huber, F.M. / Hoelz, A.
History
DepositionOct 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 60S ribosomal protein L4-like protein
B: Assembly chaperone of ribosomal protein L4 (Acl4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,48211
Polymers67,8802
Non-polymers6039
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint9 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.000, 127.900, 42.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 60S ribosomal protein L4-like protein / Ribosome


Mass: 29941.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061540 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFC3
#2: Protein Assembly chaperone of ribosomal protein L4 (Acl4)


Mass: 37937.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0010130 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0I4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS (pH 5.5) 2 % (v/v) Tacsminate (pH 5.5) 13 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 49797 / % possible obs: 99.1 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 8039 / CC1/2: 0.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.949 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2505 5.03 %
Rwork0.1891 --
obs0.1909 49766 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 39 56 4596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044632
X-RAY DIFFRACTIONf_angle_d0.7356261
X-RAY DIFFRACTIONf_dihedral_angle_d12.9361727
X-RAY DIFFRACTIONf_chiral_restr0.042690
X-RAY DIFFRACTIONf_plane_restr0.003816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.44640.33041160.29192671X-RAY DIFFRACTION98
2.4464-2.49630.33981400.26652600X-RAY DIFFRACTION100
2.4963-2.55060.26761440.26352599X-RAY DIFFRACTION99
2.5506-2.60990.3621130.2532637X-RAY DIFFRACTION99
2.6099-2.67510.26251580.24442652X-RAY DIFFRACTION100
2.6751-2.74750.29961380.22742615X-RAY DIFFRACTION100
2.7475-2.82830.27051130.24112668X-RAY DIFFRACTION100
2.8283-2.91960.30821260.23812648X-RAY DIFFRACTION100
2.9196-3.02390.28111520.23082628X-RAY DIFFRACTION100
3.0239-3.14490.25931390.23832617X-RAY DIFFRACTION99
3.1449-3.2880.28811280.23052682X-RAY DIFFRACTION100
3.288-3.46130.25541670.21942562X-RAY DIFFRACTION100
3.4613-3.67810.22241490.20822610X-RAY DIFFRACTION100
3.6781-3.96190.24341530.17762621X-RAY DIFFRACTION100
3.9619-4.36030.16461740.15382577X-RAY DIFFRACTION98
4.3603-4.99040.20281570.14972587X-RAY DIFFRACTION100
4.9904-6.28450.22261200.17812637X-RAY DIFFRACTION98
6.2845-43.95640.15331180.14122650X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.8987 Å / Origin y: -26.4995 Å / Origin z: 3.4219 Å
111213212223313233
T0.4596 Å2-0.0291 Å2-0.0311 Å2-0.4702 Å20.0331 Å2--0.4637 Å2
L1.4863 °2-0.0995 °20.222 °2-2.4835 °20.3647 °2--1.0153 °2
S0.066 Å °0.091 Å °0.0771 Å °0.3174 Å °-0.0522 Å °0.094 Å °0.0349 Å °-0.0892 Å °-0.013 Å °
Refinement TLS groupSelection details: all

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