[English] 日本語
Yorodumi
- PDB-4ncl: Crystal structure of eukaryotic translation initiation factor eIF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ncl
TitleCrystal structure of eukaryotic translation initiation factor eIF5B (517-970) from Chaetomium thermophilum in complex with GDP
ComponentsEukaryotic translation initiation factor 5B-like protein
KeywordsTRANSLATION / Translation initiation / GTPase / eIF5B/IF2 / Subunit joining / Ribosome
Function / homology
Function and homology information


protein-synthesizing GTPase / translation initiation factor activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain ...Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.115 Å
AuthorsKuhle, B. / Ficner, R.
CitationJournal: Embo J. / Year: 2014
Title: eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining.
Authors: Kuhle, B. / Ficner, R.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5B-like protein
B: Eukaryotic translation initiation factor 5B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8806
Polymers101,9452
Non-polymers9354
Water3,459192
1
A: Eukaryotic translation initiation factor 5B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4403
Polymers50,9731
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4403
Polymers50,9731
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.900, 72.960, 199.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA521 - 980
211chain BB520 - 968

-
Components

#1: Protein Eukaryotic translation initiation factor 5B-like protein


Mass: 50972.512 Da / Num. of mol.: 2 / Fragment: unp residues 516-946
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / Gene: CTHT_0029840 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S8G9
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MISMATCH (RESIDUES 576-599) IS A WRONGLY ASSIGNMENT INTRON IN THE CHAETOMIUM THERMOPHILUM ...THE MISMATCH (RESIDUES 576-599) IS A WRONGLY ASSIGNMENT INTRON IN THE CHAETOMIUM THERMOPHILUM SEQUENCE. MULTIPLE SEQUENCE ALIGNMENTS WITH HOMOLOGUES FROM OTHER SPECIES SHOWED THAT THIS INTRON CORRESPONDS TO A PROTEIN SEQUENCE, WHICH IS PRESENT AND HIGHLY CONSERVED IN ALL OTHER SPECIES. IN ADDITION, ISOLATION OF THE GENE FROM A CHAETOMIUM THERMOPHILUM CDNA LIBRARY WITH APPROPRIATE PRIMERS AMPLIFIED THE GENE INCLUDING THE WRONGLY ASSIGNED INTRON.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15 % PEG 8000, 0.5 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82658 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82658 Å / Relative weight: 1
ReflectionHighest resolution: 2.12 Å / Num. obs: 56555 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.01 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.79
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.12-2.210.6312.97199.9
2.21-2.320.4853.821100
2.32-2.520.3055.66199.7
2.52-3.340.10613.8199.7
3.34-3.740.0431.01199.6
3.74-4.160.02838.8199.6
4.16-4.570.02443.51199.6
4.57-140.01854.03199.3
14-170.01276.081100
17-500.01568.7191.6
501

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.86 Å
Translation2.5 Å47.86 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4N3N

4n3n


Resolution: 2.115→47.865 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 31.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 2828 5.01 %
Rwork0.2139 --
obs0.2157 56440 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.3775 Å2
Refinement stepCycle: LAST / Resolution: 2.115→47.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 58 192 6970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057033
X-RAY DIFFRACTIONf_angle_d0.9569510
X-RAY DIFFRACTIONf_dihedral_angle_d15.7532679
X-RAY DIFFRACTIONf_chiral_restr0.041083
X-RAY DIFFRACTIONf_plane_restr0.0041233
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3917X-RAY DIFFRACTION8.077TORSIONAL
12B3917X-RAY DIFFRACTION8.077TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.115-2.15150.3571400.31942657X-RAY DIFFRACTION100
2.1515-2.19060.38031370.29922601X-RAY DIFFRACTION100
2.1906-2.23270.32721410.28682685X-RAY DIFFRACTION100
2.2327-2.27830.32981390.28572634X-RAY DIFFRACTION100
2.2783-2.32780.32281390.26672629X-RAY DIFFRACTION100
2.3278-2.3820.33611410.25332668X-RAY DIFFRACTION100
2.382-2.44160.32131400.25182659X-RAY DIFFRACTION100
2.4416-2.50760.31941400.2522658X-RAY DIFFRACTION99
2.5076-2.58140.32031390.25072654X-RAY DIFFRACTION100
2.5814-2.66470.31921410.24352666X-RAY DIFFRACTION100
2.6647-2.75990.32261400.2452653X-RAY DIFFRACTION100
2.7599-2.87040.26541400.2412663X-RAY DIFFRACTION100
2.8704-3.0010.30261420.24132695X-RAY DIFFRACTION100
3.001-3.15920.28381410.24342678X-RAY DIFFRACTION100
3.1592-3.35710.25951410.22652667X-RAY DIFFRACTION99
3.3571-3.61620.24061410.20862677X-RAY DIFFRACTION100
3.6162-3.980.2081440.19572716X-RAY DIFFRACTION100
3.98-4.55550.19081430.16042727X-RAY DIFFRACTION100
4.5555-5.73790.17181460.1692749X-RAY DIFFRACTION99
5.7379-47.87690.2091530.18912876X-RAY DIFFRACTION99
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)
14.1872-0.5265-1.29252.85920.06483.80860.0656-0.1935-0.67730.18270.1047-0.17970.60990.1711-0.1830.47120.033-0.00710.54550.02350.4545-9.004-5.35239.6781
22.4679-0.0291-0.30571.7158-0.19533.5365-0.1335-0.15740.0424-0.01870.1003-0.2515-0.14290.43860.00350.3451-0.0484-0.00860.323-0.05990.377-3.26242.111738.9882
31.8346-0.37-0.67432.27792.37596.25820.0489-0.1071-0.00260.20870.0672-0.13740.1171-0.4226-0.19240.42120.05050.02280.45190.00870.4789-18.2137-2.54140.0793
42.37430.4712-0.16981.86581.22644.13690.01560.3189-0.16150.11160.0037-0.0409-0.0496-0.6086-0.01170.34370.0235-0.03950.44620.03360.3818-15.045-5.410628.7498
55.1796-0.546-2.52351.0939-0.12184.04270.20930.89070.2988-0.0145-0.21160.1948-0.8546-1.19510.04740.44470.131-0.06230.78840.01130.4248-22.4257-0.69423.8888
63.57871.07920.51220.7339-0.38352.83740.06230.02310.1818-0.4084-0.03910.1234-0.42930.1569-0.07320.24820.03340.00050.31210.0110.2681-10.10442.617831.3618
73.93450.6336-1.0373.2536-0.56114.03190.0446-0.1581-0.08820.1016-0.0394-0.3001-0.03490.4697-0.02170.39360.0263-0.05610.4207-0.03660.398-3.7189-0.170660.8685
83.12711.74780.45751.80890.11430.82610.0094-0.70240.52340.2748-0.19180.4494-0.0442-0.03350.1780.52290.0008-0.01490.4703-0.07630.5123-20.9311.336766.0131
93.51422.1487-0.98843.7943-0.25682.9301-0.1241-0.00540.3717-0.30460.1420.41840.3699-0.5496-0.02220.4891-0.0492-0.0460.5395-0.00260.4779-33.1919-10.539761.1854
102.8490.9047-1.74813.1464-0.74793.011-0.36010.704-0.5698-0.94580.34630.140.736-0.7750.09420.6603-0.18-0.02120.4477-0.01390.4694-33.719-19.248456.2837
112.41220.19-0.25950.76420.66384.8707-0.0499-0.3327-0.18970.20770.0301-0.04540.04910.2050.02850.33540.06540.00110.47990.04230.3715-7.8826-31.6901-5.8804
123.06310.48690.31811.48331.01494.8371-0.08050.0339-0.0552-0.02050.1106-0.0017-0.1163-0.3535-0.04770.28750.0556-0.01180.44580.0190.3402-16.4907-31.2479-17.2854
130.4423-0.4420.45752.5413-0.24723.21380.12590.15720.06140.0711-0.1951-0.31150.07460.2607-0.00460.3931-0.0012-0.04350.6165-0.01090.4619-5.6745-31.114313.0142
145.69661.06470.80151.6334-0.2061.9554-0.105-0.18050.28150.14820.04030.07650.03660.08680.06070.36160.0426-0.0160.3980.03880.2894-16.2179-36.152716.8696
152.84030.5916-0.5263.7135-0.56452.753-0.3360.1451-0.0803-0.24960.3080.07980.5881-0.1740.03210.6987-0.04810.00360.49780.00040.4557-33.0767-51.46611.9057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 521 through 544 )
2X-RAY DIFFRACTION2chain 'A' and (resid 545 through 604 )
3X-RAY DIFFRACTION3chain 'A' and (resid 605 through 626 )
4X-RAY DIFFRACTION4chain 'A' and (resid 627 through 672 )
5X-RAY DIFFRACTION5chain 'A' and (resid 673 through 709 )
6X-RAY DIFFRACTION6chain 'A' and (resid 710 through 738 )
7X-RAY DIFFRACTION7chain 'A' and (resid 739 through 826 )
8X-RAY DIFFRACTION8chain 'A' and (resid 827 through 879 )
9X-RAY DIFFRACTION9chain 'A' and (resid 880 through 929 )
10X-RAY DIFFRACTION10chain 'A' and (resid 930 through 970 )
11X-RAY DIFFRACTION11chain 'B' and (resid 520 through 626 )
12X-RAY DIFFRACTION12chain 'B' and (resid 627 through 737 )
13X-RAY DIFFRACTION13chain 'B' and (resid 738 through 782 )
14X-RAY DIFFRACTION14chain 'B' and (resid 783 through 906 )
15X-RAY DIFFRACTION15chain 'B' and (resid 907 through 968 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more