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- PDB-3cpf: Crystal structure of human eukaryotic translation initiation fact... -

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Basic information

Entry
Database: PDB / ID: 3cpf
TitleCrystal structure of human eukaryotic translation initiation factor EIF5A
ComponentsEukaryotic translation initiation factor 5A-1
KeywordsCELL CYCLE / Structural Genomics Consortium / leukemia / apoptosis / SGC / Hypusine / Initiation factor / Nucleus / Protein biosynthesis
Function / homology
Function and homology information


Hypusine synthesis from eIF5A-lysine / positive regulation of translational termination / annulate lamellae / positive regulation of translational elongation / translational elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / U6 snRNA binding / translation elongation factor activity / nuclear pore / tumor necrosis factor-mediated signaling pathway ...Hypusine synthesis from eIF5A-lysine / positive regulation of translational termination / annulate lamellae / positive regulation of translational elongation / translational elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / U6 snRNA binding / translation elongation factor activity / nuclear pore / tumor necrosis factor-mediated signaling pathway / cellular response to virus / ribosome binding / endoplasmic reticulum membrane / positive regulation of transcription by RNA polymerase II / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins ...: / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5A-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsNedyalkova, L. / Tong, Y. / Tempel, W. / Hong, B. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Nedyalkova, L. / Tong, Y. / Tempel, W. / Hong, B. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2.
Authors: Tong, Y. / Park, I. / Hong, B.S. / Nedyalkova, L. / Tempel, W. / Park, H.W.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 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 1.3Aug 30, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5A-1
B: Eukaryotic translation initiation factor 5A-1


Theoretical massNumber of molelcules
Total (without water)30,3418
Polymers30,3412
Non-polymers06
Water1629
1
A: Eukaryotic translation initiation factor 5A-1


Theoretical massNumber of molelcules
Total (without water)15,1707
Polymers15,1701
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5A-1


Theoretical massNumber of molelcules
Total (without water)15,1701
Polymers15,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.119, 76.119, 107.752
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / eIF-5A1 / Eukaryotic initiation factor 5A isoform 1 / eIF-5A / eIF-4D / Rev-binding factor


Mass: 15170.424 Da / Num. of mol.: 2 / Fragment: Residues 15-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF5A / Plasmid details: GI:134105571 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P63241
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate. Cryoprotected with 20% PEG 3350 and 20% Ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 11503 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.076 / Χ2: 1.559 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5912.80.96411231.3431100
2.59-2.6912.80.78111151.5011100
2.69-2.8112.90.52411171.4161100
2.81-2.9612.80.35811281.5471100
2.96-3.1512.90.23811361.5541100
3.15-3.3912.80.13311441.6071100
3.39-3.7312.80.08111381.8181100
3.73-4.2612.70.04811561.6551100
4.26-5.3512.60.03411781.4761100
5.35-2011.70.03412681.6621100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X6O

1x6o


Resolution: 2.5→19.996 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.22 / SU B: 25.845 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B-factors are residuals from TLS refinement. TLSMD, CNS, COOT, Molprobity programs have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.3 521 4.557 %Thin shells
Rwork0.244 ---
obs0.246 11434 99.712 %-
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: 36.775 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--1.07 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 6 9 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221915
X-RAY DIFFRACTIONr_bond_other_d0.0010.021245
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9852594
X-RAY DIFFRACTIONr_angle_other_deg1.3493.0033063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22925.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11815315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.698158
X-RAY DIFFRACTIONr_chiral_restr0.0640.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_mcbond_it0.95421277
X-RAY DIFFRACTIONr_mcbond_other0.1862524
X-RAY DIFFRACTIONr_mcangle_it1.58632024
X-RAY DIFFRACTIONr_scbond_it1.0182638
X-RAY DIFFRACTIONr_scangle_it1.5643570
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 (%)
2.5-2.56400.32881682399.149
2.564-2.6330.395720.32572179699.623
2.633-2.70800.31776276499.738
2.708-2.790.483630.32370076499.869
2.79-2.8800.29972172399.723
2.88-2.9780.472430.302661704100
2.978-3.08800.30269970099.857
3.088-3.2110.332630.29959566299.396
3.211-3.350.332520.281592644100
3.35-3.50900.25159860199.501
3.509-3.6920.294420.26955259699.664
3.692-3.9080.243380.23851855799.82
3.908-4.16600.20152753299.06
4.166-4.4840.24280.175488516100
4.484-4.8870.199260.17442745499.78
4.887-5.4240.269310.21439843099.767
5.424-6.1880.365200.239356376100
6.188-7.4030.31260.244314340100
7.403-9.8180.32990.218274283100
9.818-19.9960.19980.225194202100
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)
11.0017-0.17280.49843.5547-1.03586.7586-0.25140.25830.381-0.57450.17650.1013-0.066-0.46710.07490.11560.0242-0.17280.01060.01270.0868-64.56763.39310.021
20.1733-0.2053-0.78673.1929-2.02338.7873-0.02960.08850.142-0.6682-0.07750.53510.5948-0.65050.10710.07310.0179-0.0888-0.0554-0.02960.0334-66.57557.30913.123
31.88562.12511.89672.76990.8336.44790.202-0.78220.3234-0.17250.09360.80170.0659-1.729-0.29560.22330.097-0.32140.3581-0.00750.3307-72.85763.6897.587
425.1867-5.509312.43471.9081-2.27046.4265-0.2870.63931.0262-0.2328-0.0563-0.007-0.46630.49390.34330.0679-0.0073-0.04010.01970.0734-0.0023-51.28869.70519.603
55.20844.3796-0.560310.9203-0.66031.0568-0.2622-0.00360.13240.32640.2066-0.3429-0.28340.23670.0557-0.05740.0452-0.0436-0.0005-0.067-0.1154-41.49267.23231.979
67.1969-0.14641.12933.26040.1643.655-0.29530.4011-0.258-0.14940.2131-0.1629-0.11470.07690.0822-0.0387-0.02310.00030.0032-0.0493-0.1016-44.79160.84226.397
715.45681.26392.1777.41262.07530.7991-0.21660.1187-0.36651.22480.5437-1.0329-0.3763-0.5065-0.32710.09920.03520.00460.0812-0.03430.02516.00332.81617.929
810.3488-3.0510.09878.5002-2.8726.4056-0.0749-0.4173-1.39190.7054-0.11930.55670.8781-0.90280.19430.1868-0.17050.10230.182-0.06680.1308-6.04428.71921.57
98.86881.9525-2.338212.4961-8.15555.45490.22190.5002-2.53810.6725-0.382-0.82580.82670.05050.16010.4563-0.0204-0.05240.0985-0.05030.55633.26522.70419.862
109.667-7.4876-0.07410.30160.44430.03380.3521.27860.950.0355-0.7704-0.647-0.2085-0.14980.41840.09390.10730.12790.5005-0.04930.0233-13.09848.62315.173
114.39071.3867-4.53835.7876-1.656510.06120.27791.0061-0.0422-0.4138-0.0817-0.71320.10550.0406-0.19620.03670.10980.05420.3058-0.05870.1847-17.67849.4913.896
1210.6465-5.5428-2.36935.0404-0.16611.43650.13420.63680.1459-0.0447-0.31350.1946-0.0481-0.0760.1793-0.0130.045-0.00920.3112-0.10050.0928-16.97148.31118.815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 482 - 35
2X-RAY DIFFRACTION2AA53 - 6940 - 56
3X-RAY DIFFRACTION3AA70 - 8057 - 67
4X-RAY DIFFRACTION4AA81 - 9068 - 77
5X-RAY DIFFRACTION5AA91 - 10778 - 94
6X-RAY DIFFRACTION6AA108 - 15095 - 137
7X-RAY DIFFRACTION7BB15 - 222 - 9
8X-RAY DIFFRACTION8BB23 - 6910 - 56
9X-RAY DIFFRACTION9BB70 - 8157 - 68
10X-RAY DIFFRACTION10BB82 - 10069 - 87
11X-RAY DIFFRACTION11BB101 - 12488 - 111
12X-RAY DIFFRACTION12BB125 - 151112 - 138

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