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- PDB-3l6a: Crystal structure of the C-terminal region of Human p97 -

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Basic information

Entry
Database: PDB / ID: 3l6a
TitleCrystal structure of the C-terminal region of Human p97
ComponentsEukaryotic translation initiation factor 4 gamma 2Eukaryotic translation initiation factor 4 gamma 1
KeywordsTRANSLATION / C-terminal region / MA2 domain / W2 domain / eIF4G2 / eIF family
Function / homology
Function and homology information


macromolecule biosynthetic process / cell death / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / positive regulation of dendritic spine development / positive regulation of axon extension / translation initiation factor activity / negative regulation of autophagy / positive regulation of translation ...macromolecule biosynthetic process / cell death / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / positive regulation of dendritic spine development / positive regulation of axon extension / translation initiation factor activity / negative regulation of autophagy / positive regulation of translation / adherens junction / ISG15 antiviral mechanism / heart development / positive regulation of cell growth / regulation of cell cycle / cadherin binding / axon / mRNA binding / RNA binding / membrane / cytosol
Similarity search - Function
Initiation factor 4G / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. ...Initiation factor 4G / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Eukaryotic translation initiation factor 4 gamma 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsFan, S.
CitationJournal: Proteins / Year: 2010
Title: Crystal structure of the C-terminal region of human p97/DAP5.
Authors: Fan, S. / Jia, M.Z. / Gong, W.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 18, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.4Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4 gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0778
Polymers42,0001
Non-polymers1,0777
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.084, 102.270, 112.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Eukaryotic translation initiation factor 4 gamma 2 / Eukaryotic translation initiation factor 4 gamma 1 / eIF-4-gamma 2 / eIF-4G 2 / eIF4G 2 / p97 / Death-associated protein 5 / DAP-5


Mass: 42000.266 Da / Num. of mol.: 1 / Fragment: C-terminal region, UNP residues 540-897
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P78344

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.14 Å3/Da / Density % sol: 42.46 % / Mosaicity: 0.828 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.1M (NH4)2SO4, 0.1M MES pH 6.0, 2% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONBSRF 3W1A11.5418
ROTATING ANODERIGAKU20.9000, 0.9792
Detector
TypeIDDetectorDate
MAR CCD 130 mm1CCDAug 2, 2007
RIGAKU RAXIS IV2IMAGE PLATEOct 12, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.91
30.97921
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 22.61 / Number: 69872 / Rmerge(I) obs: 0.079 / Χ2: 1.61 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 14986 / % possible obs: 90.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955097.910.0664.7434.5
3.934.9598.910.0582.5744.7
3.443.9398.510.0621.7534.7
3.123.4496.610.0761.3384.5
2.93.1291.810.1051.1084.5
2.732.98710.1240.9084.6
2.592.7386.610.1590.8254.7
2.482.598410.1830.7464.8
2.382.4882.810.2330.6674.9
2.32.3881.710.2610.6174.8
ReflectionResolution: 2→50 Å / Num. obs: 28463 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.078 / Χ2: 1.53 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.08 Å

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
2 wavelength110.93.41-3.16
2 wavelength120.97925.55-6.63
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se28.4260.530.1360.1180.967
2Se37.1020.4380.9560.1681.321
3Se34.6870.5750.1870.1321.022
4Se27.350.460.4860.1880.823
5Se30.390.0170.490.1420.84
6Se19.1080.6180.0940.1550.708
7Se17.5040.080.4290.1340.574
8Se48.7920.4540.8170.0820.739
9Se56.2540.4810.7760.0650.924
10Se26.0420.1780.410.1570.599
Phasing dmFOM : 0.65 / FOM acentric: 0.64 / FOM centric: 0.71 / Reflection: 14653 / Reflection acentric: 12520 / Reflection centric: 2133
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-30.1970.930.940.91788498290
4.1-6.60.90.920.8522451774471
3.3-4.10.850.850.8227112295416
2.9-3.30.690.70.6426002277323
2.5-2.90.50.490.5340523618434
2.3-2.50.270.260.3522572058199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.12phasing
RESOLVE2.12phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MAD / Resolution: 2→49.45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.217 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1296 5.1 %RANDOM
Rwork0.2 ---
obs0.203 25172 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.78 Å2 / Biso mean: 27.407 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---0.59 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 67 169 3072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223019
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9984082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9415370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.61826.058137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95815575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.008157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022197
X-RAY DIFFRACTIONr_nbd_refined0.1960.21470
X-RAY DIFFRACTIONr_nbtor_refined0.30.22093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.220
X-RAY DIFFRACTIONr_mcbond_it0.6491.51858
X-RAY DIFFRACTIONr_mcangle_it1.08822905
X-RAY DIFFRACTIONr_scbond_it1.66531317
X-RAY DIFFRACTIONr_scangle_it2.6684.51166
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 106 -
Rwork0.237 1685 -
all-1791 -
obs--97.23 %

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