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- PDB-3bpj: Crystal structure of human translation initiation factor 3, subun... -

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Basic information

Entry
Database: PDB / ID: 3bpj
TitleCrystal structure of human translation initiation factor 3, subunit 1 alpha
ComponentsEukaryotic translation initiation factor 3 subunit J
KeywordsTRANSLATION / translation initiation / eif3s1 / structural genomics / limited proteolysis / Initiation factor / Phosphoprotein / Protein biosynthesis / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression ...eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / translational initiation / identical protein binding / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 3 like domains / Eukaryotic translation initiation factor 3 subunit J / Eukaryotic translation initiation factor 3-like domain superfamily / Translation initiation factor eIF3 subunit / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit J
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / molecular replacement / Resolution: 1.85 Å
AuthorsTempel, W. / Nedyalkova, L. / Hong, B. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human translation initiation factor 3, subunit 1 alpha.
Authors: Nedyalkova, L. / Hong, B. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE COMPLETE SEQUENCE OF THE CRYSTALLIZED POLYPEPTIDE IS ... SEQUENCE THE COMPLETE SEQUENCE OF THE CRYSTALLIZED POLYPEPTIDE IS MHHHHHHSSGRENLYFQGKIAEKIKEKERQQKKRQEEIKKRLEEPEEPKVLTPEEQ LADKLRLKKLQEESDLELAKETFGVNNAVYGIDAMNPSSRDDFTEFGKLLKDKITQ YEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLTVLCSEKQKQEKQSKAK FROM WHICH MHHHHHHSSGRENLYFQG IS AN EXPRESSION TAG, AND THE FOLLOWING SEQUENCE MATCHES THE FRAGMENT 76-220 OF THE UNIPROT ENTRY O75822. AUTHORS STATE THAT MANY OF THE N-TERMINAL RESIDUES WERE CLEAVED OFF PRIOR TO THE CRYSTAL FORMATION, BECAUSE OF THE PRESENCE OF CHYMOTRYPSIN IN CRYSTALLIZATION SOLUTION. THE PRECISE LOCATION OF THE CLEAVAGE SITE HAS NOT BEEN DETERMINED. THEREFORE, THE SEQUENCE INFORMATION, AS WELL AS THE VALUES OF MATTHEWS COEFFICIENT AND SOLVENT CONTENT ARE BASED ON THE CHAIN LENGTH STARTING FROM THE FIRST VISIBLE N-TERMINAL RESIDUE IN ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 3 subunit J
B: Eukaryotic translation initiation factor 3 subunit J
C: Eukaryotic translation initiation factor 3 subunit J
D: Eukaryotic translation initiation factor 3 subunit J


Theoretical massNumber of molelcules
Total (without water)36,7308
Polymers36,7304
Non-polymers04
Water90150
1
A: Eukaryotic translation initiation factor 3 subunit J
C: Eukaryotic translation initiation factor 3 subunit J


Theoretical massNumber of molelcules
Total (without water)18,3653
Polymers18,3652
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
MethodPISA
2
B: Eukaryotic translation initiation factor 3 subunit J
D: Eukaryotic translation initiation factor 3 subunit J


Theoretical massNumber of molelcules
Total (without water)18,3655
Polymers18,3652
Non-polymers03
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.902, 62.373, 88.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Eukaryotic translation initiation factor 3 subunit J / Eukaryotic translation initiation factor 3 subunit 1 / eIF-3-alpha / eIF3 p35 / eIF3j


Mass: 9182.524 Da / Num. of mol.: 4 / Fragment: Proteolytic fragment: Residues 141-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3J, EIF3S1, PRO0391 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O75822
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.97 %
Description: A heavy atom derivative was prepared by overnight soaking of a protein crystal in a 1:19 mixture of 0.2M thimerosal and cryoprotectant (25% PEG 3350, 10% PEG, 0.1M Sodium acetate pH 4.6). ...Description: A heavy atom derivative was prepared by overnight soaking of a protein crystal in a 1:19 mixture of 0.2M thimerosal and cryoprotectant (25% PEG 3350, 10% PEG, 0.1M Sodium acetate pH 4.6). Diffraction intensities for this derivative are deposited with crystal index 2 (index 1 for native intensities).
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% PEG 3350, 0.1M Sodium acetate. Chymotrypsin was added to the crystallization sample at a molar ratio of approx. 1:100, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E11.5418
ROTATING ANODERIGAKU FR-E21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS1IMAGE PLATEDec 17, 2007
RIGAKU RAXIS2IMAGE PLATEDec 14, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 29322 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.041 / Χ2: 1.813 / Net I/σ(I): 24.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.927.20.87728761.5381,2100
1.92-1.997.30.59728771.5981,2100
1.99-2.087.30.34929021.681,2100
2.08-2.197.40.19629011.7751,2100
2.19-2.337.40.13229141.821,2100
2.33-2.517.50.08629161.8591,2100
2.51-2.767.50.05229421.7921,2100
2.76-3.167.50.03629531.721,2100
3.16-3.987.40.03129661.7871,299.2
3.98-306.90.03530752.5641,298.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
REFMAC5.3.0037refinement
PDB_EXTRACT3.004data extraction
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.242 / SU B: 7.622 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B factors are residuals from TLS refinement. Programs resolve, arp/warp, coot, molprobity have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1442 4.947 %thin shells (from program SFTOOLS)
Rwork0.229 ---
obs0.23 29151 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.914 Å2
Baniso -1Baniso -2Baniso -3
1--0.208 Å20 Å20 Å2
2---0.654 Å20 Å2
3---0.862 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 4 50 2177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222155
X-RAY DIFFRACTIONr_bond_other_d0.0010.021391
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.992917
X-RAY DIFFRACTIONr_angle_other_deg0.94733437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.24225.31679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.822156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
X-RAY DIFFRACTIONr_nbd_refined0.2290.2491
X-RAY DIFFRACTIONr_nbd_other0.1680.21386
X-RAY DIFFRACTIONr_nbtor_refined0.180.21144
X-RAY DIFFRACTIONr_nbtor_other0.0890.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3690.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.24
X-RAY DIFFRACTIONr_mcbond_it2.39221445
X-RAY DIFFRACTIONr_mcbond_other0.7722568
X-RAY DIFFRACTIONr_mcangle_it3.21432256
X-RAY DIFFRACTIONr_scbond_it2.7742801
X-RAY DIFFRACTIONr_scangle_it3.8523661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8980.2981130.2551970208899.761
1.898-1.9490.2651320.2581944208099.808
1.949-2.0060.2851100.2451897201299.751
2.006-2.0670.2510.2231950195299.949
2.067-2.1340.2811480.2151746189699.895
2.134-2.2090.367200.221835185799.892
2.209-2.2910.2821140.22116621776100
2.291-2.3840.2681230.221596172099.942
2.384-2.4890.3011070.2281548165799.879
2.489-2.60900.2351556155999.808
2.609-2.7490.2831040.2481409151699.802
2.749-2.9130.293890.2431344143599.861
2.913-3.1110.323720.2481278135599.631
3.111-3.3560.301670.2641186125699.761
3.356-3.670.277620.2341111118199.323
3.67-4.0920.223400.1971008106098.868
4.092-4.7040.262350.18889095996.455
4.704-5.7110.23510.22576081799.266
5.711-7.8740.214350.30963467099.851
7.874-250.212190.19738542295.735
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)
14.3881.00521.12091.6960.60344.7569-0.0110.06160.048-0.07910.05360.1036-0.05450.0104-0.0425-0.14340.0373-0.0367-0.0696-0.011-0.176715.078-13.767-5.946
22.2293-1.31970.92455.00150.33353.2281-0.08350.08840.0839-0.37860.06490.3171-0.1761-0.16370.01860.0475-0.0525-0.098-0.17130.0378-0.19130.373-9.904-26.912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA144 - 2134 - 73
2X-RAY DIFFRACTION1CC144 - 2164 - 76
3X-RAY DIFFRACTION2BB141 - 2111 - 71
4X-RAY DIFFRACTION2DD144 - 2124 - 72

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