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- PDB-3krm: Imp1 kh34 -

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Basic information

Entry
Database: PDB / ID: 3krm
TitleImp1 kh34
ComponentsInsulin-like growth factor 2 mRNA-binding protein 1
KeywordsRNA BINDING PROTEIN / KH domain / Cell projection / Cytoplasm / Nucleus / Phosphoprotein / RNA-binding / Translation regulation
Function / homology
Function and homology information


regulation of mRNA stability involved in response to stress / pallium cell proliferation in forebrain / Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / dendrite arborization / CRD-mediated mRNA stabilization / neuronal stem cell population maintenance / N6-methyladenosine-containing RNA reader activity / positive regulation of cytoplasmic translation ...regulation of mRNA stability involved in response to stress / pallium cell proliferation in forebrain / Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / dendrite arborization / CRD-mediated mRNA stabilization / neuronal stem cell population maintenance / N6-methyladenosine-containing RNA reader activity / positive regulation of cytoplasmic translation / mRNA transport / translation regulator activity / regulation of cytokine production / filopodium / mRNA 3'-UTR binding / P-body / MAPK6/MAPK4 signaling / mRNA 5'-UTR binding / cytoplasmic stress granule / lamellipodium / nervous system development / growth cone / regulation of gene expression / dendritic spine / negative regulation of translation / ribonucleoprotein complex / mRNA binding / neuronal cell body / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
TATA-Binding Protein - #210 / IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / TATA-Binding Protein / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif ...TATA-Binding Protein - #210 / IGF2BP1, RNA recognition motif 1 / IGF2BP1, RNA recognition motif 2 / KH domain / K Homology domain, type 1 / TATA-Binding Protein / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Insulin-like growth factor 2 mRNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.75 Å
AuthorsChao, J.A. / Singer, R.H. / Almo, S.C. / Patskovsky, Y.
CitationJournal: Genes Dev. / Year: 2010
Title: ZBP1 recognition of beta-actin zipcode induces RNA looping.
Authors: Chao, J.A. / Patskovsky, Y. / Patel, V. / Levy, M. / Almo, S.C. / Singer, R.H.
History
DepositionNov 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin-like growth factor 2 mRNA-binding protein 1
B: Insulin-like growth factor 2 mRNA-binding protein 1
C: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4527
Polymers54,0843
Non-polymers3684
Water00
1
A: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2123
Polymers18,0281
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2123
Polymers18,0281
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin-like growth factor 2 mRNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)18,0281
Polymers18,0281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules

A: Insulin-like growth factor 2 mRNA-binding protein 1
C: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4527
Polymers54,0843
Non-polymers3684
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation6_554x-y,x,z-1/61
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-22 kcal/mol
Surface area22430 Å2
MethodPISA
5
A: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules

B: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4246
Polymers36,0562
Non-polymers3684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area15840 Å2
MethodPISA
6
A: Insulin-like growth factor 2 mRNA-binding protein 1
C: Insulin-like growth factor 2 mRNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2404
Polymers36,0562
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-7 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.530, 103.530, 131.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsGel filtration data that show the protein is monomeric in solution

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Components

#1: Protein Insulin-like growth factor 2 mRNA-binding protein 1 / IGF2 mRNA-binding protein 1 / IMP-1 / IGF-II mRNA-binding protein 1 / Coding region determinant- ...IGF2 mRNA-binding protein 1 / IMP-1 / IGF-II mRNA-binding protein 1 / Coding region determinant-binding protein / CRD-BP / VICKZ family member 1 / Zip code-binding protein 1 / Zipcode-binding protein 1 / ZBP-1


Mass: 18027.838 Da / Num. of mol.: 3 / Fragment: residues 404-566
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2BP1, CRDBP, VICKZ1, ZBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9NZI8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.76 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 1.65M Ammonium Citrate, 100mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→53 Å / Num. obs: 20824 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3010 / % possible all: 100

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Processing

Software
NameClassification
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.75→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1043 -RANDOM
Rwork0.1977 ---
all0.1999 20808 --
obs0.1999 20304 5.14 %-
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 24 0 3650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.227
X-RAY DIFFRACTIONf_bond_d0.012

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