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- PDB-6gqe: X-ray structure of KH1-2 domain of IMP3 -

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Basic information

Entry
Database: PDB / ID: 6gqe
TitleX-ray structure of KH1-2 domain of IMP3
ComponentsInsulin-like growth factor 2 mRNA-binding protein 3
KeywordsRNA BINDING PROTEIN / multidomain-RNA binding protein / insulin-like growth factor 2 / mRNA binding protein 3 (IMP3) / mRNA-protein interactions
Function / homology
Function and homology information


Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / translation regulator activity / mRNA transport / anatomical structure morphogenesis / regulation of cytokine production / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding ...Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / translation regulator activity / mRNA transport / anatomical structure morphogenesis / regulation of cytokine production / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / nervous system development / regulation of gene expression / negative regulation of translation / translation / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
IGF2BP3, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...IGF2BP3, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / K Homology domain / K homology RNA-binding domain / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Insulin-like growth factor 2 mRNA binding protein 3 / Insulin-like growth factor 2 mRNA-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJanowski, R. / Schlundt, A. / Sattler, M. / Niessing, D.
CitationJournal: Nat Commun / Year: 2019
Title: Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3.
Authors: Schneider, T. / Hung, L.H. / Aziz, M. / Wilmen, A. / Thaum, S. / Wagner, J. / Janowski, R. / Muller, S. / Schreiner, S. / Friedhoff, P. / Huttelmaier, S. / Niessing, D. / Sattler, M. / ...Authors: Schneider, T. / Hung, L.H. / Aziz, M. / Wilmen, A. / Thaum, S. / Wagner, J. / Janowski, R. / Muller, S. / Schreiner, S. / Friedhoff, P. / Huttelmaier, S. / Niessing, D. / Sattler, M. / Schlundt, A. / Bindereif, A.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jun 5, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Aug 14, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.4Jan 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

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Assembly

Deposited unit
A: Insulin-like growth factor 2 mRNA-binding protein 3


Theoretical massNumber of molelcules
Total (without water)18,6261
Polymers18,6261
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.200, 58.090, 60.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 3 / IMP-3 / IGF-II mRNA-binding protein 3 / KH domain-containing protein overexpressed in cancer / hKOC ...IMP-3 / IGF-II mRNA-binding protein 3 / KH domain-containing protein overexpressed in cancer / hKOC / VICKZ family member 3


Mass: 18626.416 Da / Num. of mol.: 1 / Mutation: K294D, E295D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2BP3, IMP3, KOC1, VICKZ3 / Production host: Escherichia coli (E. coli) / References: UniProt: O00425, UniProt: A0A0B8RZH0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08 M magnesium acetate, 0.05 M sodium cacodylate pH 6.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 7366 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.94
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.63 / CC1/2: 0.767 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ann

2ann


Resolution: 2.15→42.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 28.983 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.293 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29273 848 11.5 %RANDOM
Rwork0.23287 ---
obs0.23976 6518 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.272 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å2-0 Å2-0 Å2
2---2.14 Å20 Å2
3---6.13 Å2
Refinement stepCycle: 1 / Resolution: 2.15→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 0 16 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191301
X-RAY DIFFRACTIONr_bond_other_d0.0020.021272
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9821753
X-RAY DIFFRACTIONr_angle_other_deg0.89932978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44825.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.547157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7463.877655
X-RAY DIFFRACTIONr_mcbond_other1.7473.876654
X-RAY DIFFRACTIONr_mcangle_it2.8815.801817
X-RAY DIFFRACTIONr_mcangle_other2.885.803818
X-RAY DIFFRACTIONr_scbond_it1.6134.144646
X-RAY DIFFRACTIONr_scbond_other1.6124.146647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7356.136936
X-RAY DIFFRACTIONr_long_range_B_refined4.61746.9151399
X-RAY DIFFRACTIONr_long_range_B_other4.61546.9371400
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å
RfactorNum. reflection% reflection
Rfree0.361 58 -
Rwork0.35 452 -
obs--100 %

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