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- PDB-1ha1: HNRNP A1 (RBD1,2) FROM HOMO SAPIENS -

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Basic information

Entry
Database: PDB / ID: 1ha1
TitleHNRNP A1 (RBD1,2) FROM HOMO SAPIENS
ComponentsHNRNP A1
KeywordsNUCLEAR PROTEIN / HNRNP / RBD / RRM / RNP / RNA BINDING / RIBONUCLEOPROTEIN
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of telomere maintenance via telomerase / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.75 Å
AuthorsShamoo, Y. / Krueger, U. / Rice, L. / Williams, K.R. / Steitz, T.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 A resolution.
Authors: Shamoo, Y. / Krueger, U. / Rice, L.M. / Williams, K.R. / Steitz, T.A.
#1: Journal: Biochemistry / Year: 1994
Title: Determination of the Secondary Structure and Folding Topology of an RNA Binding Domain of Mammalian Hnrnp A1 Protein Using Three-Dimensional Heteronuclear Magnetic Resonance Spectroscopy
Authors: Garrett, D.S. / Lodi, P.J. / Shamoo, Y. / Williams, K.R. / Clore, G.M. / Gronenborn, A.M.
History
DepositionOct 30, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HNRNP A1


Theoretical massNumber of molelcules
Total (without water)21,0531
Polymers21,0531
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.600, 43.500, 55.500
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HNRNP A1 / HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 / HNRNP A1 1-184


Mass: 21052.734 Da / Num. of mol.: 1 / Fragment: HNRNP A1 (RBD1, RBD2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Plasmid: PA1_1-184 / Production host: Escherichia coli (E. coli) / References: UniProt: P09651
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.15 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.1
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 1500, 50 MM NACL, 20 MM TRIS 8.1, THEN MOVED TO 15% ETHYLENE GLYCOL FOR FREEZING.
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlRBD1,21drop
250 mM1dropNaCl
330 mMTris1drop
414-16 %PEG15001drop
550 mM1reservoirNaCl
650 mMTris1reservoir
728-32 %PEG15001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.35
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jun 1, 1996 / Details: BENDING MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 18507 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 4.3
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.223 / % possible all: 66.2
Reflection
*PLUS
Num. measured all: 42714

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR / Resolution: 1.75→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1485 9.9 %RANDOM
Rwork0.198 ---
obs0.198 15067 83.7 %-
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.15 Å2
2--0.23 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 170 1508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.791.5
X-RAY DIFFRACTIONx_mcangle_it2.82
X-RAY DIFFRACTIONx_scbond_it3.312
X-RAY DIFFRACTIONx_scangle_it5.052.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 167 9.7 %
Rwork0.296 1549 -
obs--57.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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