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- PDB-6h7b: Structure of Leishmania PABP1 (domain J) complexed with a peptide... -

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Basic information

Entry
Database: PDB / ID: 6h7b
TitleStructure of Leishmania PABP1 (domain J) complexed with a peptide containing the PAM2 motif of eIF4E4.
Components
  • HIS-HIS-MET-ASN-PRO-ASN-ALA-THR-GLU-PHE-MET-PRO
  • Polyadenylate-binding protein
KeywordsTRANSLATION / Complex Translation Initiation Leishmania
Function / homology
Function and homology information


eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / poly(A) binding / poly(U) RNA binding / : / translation initiation factor activity / mRNA 3'-UTR binding ...eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / poly(A) binding / poly(U) RNA binding / : / translation initiation factor activity / mRNA 3'-UTR binding / cytoplasmic stress granule / ribonucleoprotein complex / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Translation Initiation factor eIF- 4e ...c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyadenylate-binding protein / Putative eukaryotic translation initiation factor 4e
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsCameron, A.D. / Firczuk, H. / dos Santos Rodrigues, F.H. / McCarthy, J.E.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N017447/1 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The Leishmania PABP1-eIF4E4 interface: a novel 5'-3' interaction architecture for trans-spliced mRNAs.
Authors: Dos Santos Rodrigues, F.H. / Firczuk, H. / Breeze, A.L. / Cameron, A.D. / Walko, M. / Wilson, A.J. / Zanchin, N.I.T. / McCarthy, J.E.G.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyadenylate-binding protein
B: HIS-HIS-MET-ASN-PRO-ASN-ALA-THR-GLU-PHE-MET-PRO
C: Polyadenylate-binding protein
D: HIS-HIS-MET-ASN-PRO-ASN-ALA-THR-GLU-PHE-MET-PRO


Theoretical massNumber of molelcules
Total (without water)24,8994
Polymers24,8994
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-29 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.330, 83.330, 58.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Polyadenylate-binding protein / PABP


Mass: 10807.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PABP1, LMJF_35_5040 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): NiCo21 / References: UniProt: E9AFX7
#2: Protein/peptide HIS-HIS-MET-ASN-PRO-ASN-ALA-THR-GLU-PHE-MET-PRO


Mass: 1641.850 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Leishmania major (eukaryote) / References: UniProt: Q4Q7R3*PLUS
#3: Water ChemComp-HOH / water / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium sulphate; 0.1M MES; 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.89→36.1 Å / Num. obs: 18507 / % possible obs: 99.87 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.01918 / Rrim(I) all: 0.06019 / Net I/σ(I): 18.54
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.5 / Num. unique obs: 1829 / CC1/2: 0.586 / Rpim(I) all: 0.5737 / Rrim(I) all: 1.607 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H7A

6h7a


Resolution: 1.89→36.083 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3
RfactorNum. reflection% reflection
Rfree0.2295 920 4.97 %
Rwork0.1972 --
obs0.1989 18505 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→36.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 50 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041476
X-RAY DIFFRACTIONf_angle_d0.5831995
X-RAY DIFFRACTIONf_dihedral_angle_d16.928946
X-RAY DIFFRACTIONf_chiral_restr0.039221
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8901-1.98970.32181210.3112523X-RAY DIFFRACTION100
1.9897-2.11440.3021120.25972496X-RAY DIFFRACTION100
2.1144-2.27760.27191540.23152465X-RAY DIFFRACTION100
2.2776-2.50670.23661270.21462519X-RAY DIFFRACTION100
2.5067-2.86930.25451310.22962502X-RAY DIFFRACTION100
2.8693-3.61450.27671430.21922520X-RAY DIFFRACTION100
3.6145-36.08950.18091320.15852560X-RAY DIFFRACTION100
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)
19.7369-1.7832-3.41882.15710.45192.6382-0.1596-0.0666-0.09960.20840.11590.09580.1279-0.17450.04750.28190.0182-0.03980.35610.04340.29973.5607-30.49951.8426
28.0913-4.7669-3.20772.94771.05737.5223-0.15690.9823-0.3590.20250.02630.12830.0231-0.90620.10350.4752-0.0577-0.09190.54440.03830.50866.2364-31.9751-7.5274
34.74055.55051.70499.4912.30631.23250.01010.0617-0.3689-0.2426-0.0205-0.22150.2661-0.15150.03210.3512-0.00750.01840.33860.02930.346218.5258-52.5208-4.9111
41.34830.3335-2.15219.52713.95766.91120.1992-0.2377-0.08770.69750.23280.03110.5221-0.3833-0.33010.5279-0.0889-0.07320.57460.17010.514118.5915-49.32574.2588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 482 through 559)
2X-RAY DIFFRACTION2(chain 'B' and resid 138 through 149)
3X-RAY DIFFRACTION3(chain 'C' and resid 482 through 558)
4X-RAY DIFFRACTION4(chain 'D' and resid 138 through 149)

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