[English] 日本語
Yorodumi
- PDB-4dpg: Crystal Structure of Human LysRS: P38/AIMP2 Complex I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dpg
TitleCrystal Structure of Human LysRS: P38/AIMP2 Complex I
Components
  • Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
  • Lysine--tRNA ligase
KeywordsLigase/APOPTOSIS / lysyl-tRNA synthetase / LysRS / P38 / AIMP2 / multi tRNA synthetase complex sub-complex / Ligase-APOPTOSIS complex
Function / homology
Function and homology information


ATP:ADP adenylyltransferase activity / type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process ...ATP:ADP adenylyltransferase activity / type II pneumocyte differentiation / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / ERK1 and ERK2 cascade / positive regulation of protein ubiquitination / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein-containing complex assembly / tRNA binding / molecular adaptor activity / protein ubiquitination / mitochondrial matrix / translation / negative regulation of cell population proliferation / apoptotic process / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) ...AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Glutathione S-transferase, C-terminal domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Glutathione S-transferase, C-terminal / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ALANINE / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / LYSINE / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.844 Å
AuthorsFang, P. / Wang, J. / Bennett, S.P. / Guo, M.
CitationJournal: Mol.Cell / Year: 2013
Title: Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.
Authors: Ofir-Birin, Y. / Fang, P. / Bennett, S.P. / Zhang, H.M. / Wang, J. / Rachmin, I. / Shapiro, R. / Song, J. / Dagan, A. / Pozo, J. / Kim, S. / Marshall, A.G. / Schimmel, P. / Yang, X.L. / ...Authors: Ofir-Birin, Y. / Fang, P. / Bennett, S.P. / Zhang, H.M. / Wang, J. / Rachmin, I. / Shapiro, R. / Song, J. / Dagan, A. / Pozo, J. / Kim, S. / Marshall, A.G. / Schimmel, P. / Yang, X.L. / Nechushtan, H. / Razin, E. / Guo, M.
History
DepositionFeb 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_auth_seq_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_conn.ptnr2_label_seq_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: Lysine--tRNA ligase
B: Lysine--tRNA ligase
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
E: Lysine--tRNA ligase
F: Lysine--tRNA ligase
G: Lysine--tRNA ligase
H: Lysine--tRNA ligase
I: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
J: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
K: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
L: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)503,81341
Polymers498,21312
Non-polymers5,60029
Water9,764542
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
I: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9079
Polymers124,5533
Non-polymers1,3536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-93 kcal/mol
Surface area39310 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
K: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9079
Polymers124,5533
Non-polymers1,3536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-90 kcal/mol
Surface area39730 Å2
MethodPISA
3
E: Lysine--tRNA ligase
F: Lysine--tRNA ligase
L: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,95511
Polymers124,5533
Non-polymers1,4028
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-92 kcal/mol
Surface area39370 Å2
MethodPISA
4
G: Lysine--tRNA ligase
H: Lysine--tRNA ligase
J: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,04412
Polymers124,5533
Non-polymers1,4919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-91 kcal/mol
Surface area39180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.200, 122.010, 149.200
Angle α, β, γ (deg.)89.160, 85.580, 89.710
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 59240.133 Da / Num. of mol.: 8 / Fragment: UNP residues 70-581
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS, KIAA0070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15046, lysine-tRNA ligase
#2: Protein
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 6072.879 Da / Num. of mol.: 4 / Fragment: UNP residues 1-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13155

-
Non-polymers , 5 types, 571 molecules

#3: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 22% PEG10000, 0.1 M MES pH 6.7, 0.1 M magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.844→50 Å / Num. obs: 128809 / % possible obs: 99.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.102 / Χ2: 0.79 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.844-2.9640.487127500.659198.6
2.96-3.0840.377128410.682198.7
3.08-3.2240.283128290.699198.8
3.22-3.3940.211128910.732198.9
3.39-3.640.153128900.788199
3.6-3.8840.108128220.846199.1
3.88-4.2740.08129570.909199.3
4.27-4.8940.059129380.97199.4
4.89-6.1640.06129360.846199.5
6.16-503.90.036129550.768199.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.844→46.836 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8517 / SU ML: 0.76 / σ(F): 1.98 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 6481 5.03 %
Rwork0.1847 --
obs0.1866 128750 98.47 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.242 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 160.2 Å2 / Biso mean: 42.3954 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.6703 Å20.023 Å20.129 Å2
2---0.0959 Å20.3519 Å2
3---1.7662 Å2
Refinement stepCycle: LAST / Resolution: 2.844→46.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32869 0 329 542 33740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133987
X-RAY DIFFRACTIONf_angle_d1.19446074
X-RAY DIFFRACTIONf_chiral_restr0.0795034
X-RAY DIFFRACTIONf_plane_restr0.0065948
X-RAY DIFFRACTIONf_dihedral_angle_d17.89312723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.844-2.87680.34131800.29423307348781
2.8768-2.91060.34482260.27454120434699
2.9106-2.94610.32121890.25874115430499
2.9461-2.98340.32172030.24674069427299
2.9834-3.02260.28142050.24894110431599
3.0226-3.0640.29272240.23554068429299
3.064-3.10780.2952060.22584106431299
3.1078-3.15420.2491920.21454124431699
3.1542-3.20340.26882020.22044086428899
3.2034-3.25590.24522290.21614071430099
3.2559-3.31210.25962140.20514146436099
3.3121-3.37230.23332340.20934014424899
3.3723-3.43710.30532110.20854124433599
3.4371-3.50730.2372240.19814047427199
3.5073-3.58350.22752110.19434134434599
3.5835-3.66680.22452250.18964079430499
3.6668-3.75850.22572300.17984124435499
3.7585-3.86010.20812040.17134077428199
3.8601-3.97360.21212180.16164142436099
3.9736-4.10180.20862310.16374072430399
4.1018-4.24830.1791990.15084146434599
4.2483-4.41830.18872300.14064125435599
4.4183-4.61920.17562080.13754091429999
4.6192-4.86250.182530.13854112436599
4.8625-5.16680.18262440.15274068431299
5.1668-5.56510.22862070.180441494356100
5.5651-6.1240.24432270.19841154342100
6.124-7.00770.19532100.198441134323100
7.0077-8.81930.17842200.157541524372100
8.8193-46.84210.16822250.16854063428899
Refinement TLS params.Method: refined / Origin x: 32.2323 Å / Origin y: 23.8039 Å / Origin z: 0.4876 Å
111213212223313233
T0.0899 Å20.0031 Å2-0.002 Å2-0.1723 Å2-0.0105 Å2--0.1874 Å2
L0.0181 °20.0044 °2-0.0034 °2-0.0911 °2-0.0648 °2--0.286 °2
S0.0125 Å °-0.0015 Å °0.003 Å °0.0053 Å °-0.0132 Å °-0.0215 Å °0.0032 Å °0.0123 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA71 - 701
2X-RAY DIFFRACTION1allB71 - 701
3X-RAY DIFFRACTION1allC71 - 701
4X-RAY DIFFRACTION1allD71 - 701
5X-RAY DIFFRACTION1allE72 - 701
6X-RAY DIFFRACTION1allF71 - 701
7X-RAY DIFFRACTION1allG72 - 701
8X-RAY DIFFRACTION1allH71 - 701
9X-RAY DIFFRACTION1allI2 - 32
10X-RAY DIFFRACTION1allJ2 - 32
11X-RAY DIFFRACTION1allK2 - 32
12X-RAY DIFFRACTION1allL2 - 32
13X-RAY DIFFRACTION1allD1 - 603
14X-RAY DIFFRACTION1allA1 - 603
15X-RAY DIFFRACTION1allE1 - 603
16X-RAY DIFFRACTION1allG1 - 603
17X-RAY DIFFRACTION1allB1 - 603
18X-RAY DIFFRACTION1allC1 - 603
19X-RAY DIFFRACTION1allF1 - 603
20X-RAY DIFFRACTION1allH1 - 604
21X-RAY DIFFRACTION1allH1 - 605
22X-RAY DIFFRACTION1allJ1 - 101
23X-RAY DIFFRACTION1allF1 - 604
24X-RAY DIFFRACTION1allL1 - 101
25X-RAY DIFFRACTION1allG - D1 - 771

+
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