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- PDB-6dhs: Structure of hnRNP H qRRM1,2 -

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Basic information

Entry
Database: PDB / ID: 6dhs
TitleStructure of hnRNP H qRRM1,2
ComponentsHeterogeneous nuclear ribonucleoprotein H
KeywordsSPLICING / HNRNPH / alternative splicing / RNA recognition motif
Function / homology
Function and homology information


poly(U) RNA binding / FGFR2 alternative splicing / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding ...poly(U) RNA binding / FGFR2 alternative splicing / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
Zinc finger, CHHC-type / RNPHF zinc finger / 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 ...Zinc finger, CHHC-type / RNPHF zinc finger / 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 H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM101979 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U54GM103297 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Differential Conformational Dynamics Encoded by the Inter-qRRM linker of hnRNP H.
Authors: Penumutchu, S. / Chiu, L.Y. / Meagher, J.L. / Hansen, A.L. / Stuckey, J.A. / Tolbert, B.S.
History
DepositionMay 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein H
B: Heterogeneous nuclear ribonucleoprotein H
C: Heterogeneous nuclear ribonucleoprotein H
D: Heterogeneous nuclear ribonucleoprotein H


Theoretical massNumber of molelcules
Total (without water)85,5874
Polymers85,5874
Non-polymers00
Water0
1
A: Heterogeneous nuclear ribonucleoprotein H


Theoretical massNumber of molelcules
Total (without water)21,3971
Polymers21,3971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heterogeneous nuclear ribonucleoprotein H


Theoretical massNumber of molelcules
Total (without water)21,3971
Polymers21,3971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heterogeneous nuclear ribonucleoprotein H


Theoretical massNumber of molelcules
Total (without water)21,3971
Polymers21,3971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heterogeneous nuclear ribonucleoprotein H


Theoretical massNumber of molelcules
Total (without water)21,3971
Polymers21,3971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)204.670, 204.670, 123.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein
Heterogeneous nuclear ribonucleoprotein H / hnRNP H


Mass: 21396.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPH1, HNRPH, HNRPH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31943

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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: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30-50% peg 400 and 0.1M phosphate-citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 21278 / % possible obs: 100 % / Redundancy: 30.9 % / Biso Wilson estimate: 40.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.027 / Rrim(I) all: 0.15 / Χ2: 0.999 / Net I/σ(I): 5.7 / Num. measured all: 606047
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.5631.30.8359530.9450.150.8480.767100
3.56-3.6331.40.7259560.9490.130.7370.802100
3.63-3.6931.40.6379530.9660.1140.6480.808100
3.69-3.7731.30.5719630.9680.1020.580.814100
3.77-3.8531.30.4979760.9740.0890.5050.868100
3.85-3.9431.40.4199410.980.0750.4250.921100
3.94-4.0431.40.3419660.9840.0610.3460.997100
4.04-4.1531.30.2999640.990.0540.3041.033100
4.15-4.2731.20.2549710.9940.0460.2591.081100
4.27-4.4131.20.2249700.9940.0410.2281.155100
4.41-4.5731.30.1979630.9950.0360.2011.221100
4.57-4.7531.10.1819750.9960.0330.1841.176100
4.75-4.9731.30.1729720.9960.0310.1751.208100
4.97-5.2331.30.1569710.9970.0280.1581.201100
5.23-5.5531.30.1359900.9970.0250.1371.137100
5.55-5.9831.30.1149840.9980.0210.1161.083100
5.98-6.5831.20.1049980.9990.0190.1050.987100
6.58-7.5330.80.08910010.9980.0160.090.991100
7.53-9.4829.50.07910330.9990.0140.080.948100
9.48-5026.50.06711040.9990.0130.0690.75899.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 3.5→45.69 Å / Cor.coef. Fo:Fc: 0.745 / Cor.coef. Fo:Fc free: 0.718 / SU R Cruickshank DPI: 1.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.361 / SU Rfree Blow DPI: 0.515 / SU Rfree Cruickshank DPI: 0.524
RfactorNum. reflection% reflectionSelection details
Rfree0.322 902 4.57 %RANDOM
Rwork0.306 ---
obs0.306 19753 99.9 %-
Displacement parametersBiso max: 239.77 Å2 / Biso mean: 56 Å2 / Biso min: 16.33 Å2
Baniso -1Baniso -2Baniso -3
1--10.9419 Å20 Å20 Å2
2---10.9419 Å20 Å2
3---21.8838 Å2
Refine analyzeLuzzati coordinate error obs: 0.78 Å
Refinement stepCycle: final / Resolution: 3.5→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 0 0 4281
Num. residues----697
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1750SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes799HARMONIC5
X-RAY DIFFRACTIONt_it4370HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion659SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4394SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4370HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5994HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion1.89
LS refinement shellResolution: 3.5→3.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 45
RfactorNum. reflection% reflection
Rfree0.3425 14 3.19 %
Rwork0.3811 425 -
all0.3797 439 -
obs--99.55 %
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)
15.30383.8076-1.77292.6287-0.25840-0.01910.06860.1217-0.20130.01930.11110.09820.6188-0.0002-0.2975-0.16310.00010.2418-0.17540.2697-28.812572.3214-0.9737
23.70493.67282.80566.18530.96140-0.0203-0.00840.2135-0.1890.04540.01750.08980.1046-0.0252-0.1461-0.0879-0.0894-0.3956-0.1490.304-51.363574.3654-1.7797
38.43561.0157-0.56792.25143.03284.2919-0.18590.25490.2480.2063-0.1338-0.0071-0.2176-0.36750.3197-0.1133-0.1519-0.0556-0.2889-0.20760.2804-47.580374.370824.853
48.72741.89651.10160.03683.78610-0.02520.0056-0.0606-0.0797-0.02320.0930.0970.04140.0485-0.291-0.1744-0.20320.26130.04810.2991-29.618888.192120.2104
57.65121.507-1.0653-0.8102-3.97577.45570.10750.05940.0522-0.2923-0.21620.0533-0.44220.29720.1088-0.2907-0.0701-0.14810.1412-0.04750.3044.442888.8877-45.9111
610.3729-0.65322.21354.4059-2.08270.50450.0072-0.11630.1209-0.18450.11980.0647-0.23530.1455-0.1269-0.34260.034-0.1124-0.0309-0.10920.2958-18.440491.3637-41.5176
76.3346-0.8799-0.62720.6294-3.72270.9443-0.0896-0.07330.15560.3265-0.14580.0930.3613-0.16740.2354-0.0433-0.0256-0.18590.33730.06820.2903-11.358676.6854-20.497
87.637-1.11132.08262.19882.213600.0708-0.10070.07110.03370.0010.0345-0.2245-0.0336-0.0718-0.3172-0.0448-0.17590.08560.01690.29497.378990.5792-18.6966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|12 - 99}A12 - 99
2X-RAY DIFFRACTION2{A|109 - 194}A109 - 194
3X-RAY DIFFRACTION3{B|12 - 102}B12 - 102
4X-RAY DIFFRACTION4{B|110 - 194}B110 - 194
5X-RAY DIFFRACTION5{C|12 - 102}C12 - 102
6X-RAY DIFFRACTION6{C|110 - 191}C110 - 191
7X-RAY DIFFRACTION7{D|12 - 99}D12 - 99
8X-RAY DIFFRACTION8{D|110 - 194}D110 - 194

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