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- PDB-7wm3: hnRNP A2/B1 RRMs in complex with single-stranded DNA -

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Basic information

Entry
Database: PDB / ID: 7wm3
TitlehnRNP A2/B1 RRMs in complex with single-stranded DNA
Components
  • DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
  • Heterogeneous nuclear ribonucleoproteins A2/B1
KeywordsDNA BINDING PROTEIN/DNA / homodimerization / U-shaped structured DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


miRNA transport / RNA transport / positive regulation of telomere maintenance via telomere lengthening / DNA geometric change / primary miRNA processing / N6-methyladenosine-containing RNA reader activity / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / miRNA binding / Processing of Capped Intron-Containing Pre-mRNA ...miRNA transport / RNA transport / positive regulation of telomere maintenance via telomere lengthening / DNA geometric change / primary miRNA processing / N6-methyladenosine-containing RNA reader activity / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / miRNA binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / mRNA export from nucleus / Cajal body / DNA polymerase binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA 3'-UTR binding / spliceosomal complex / molecular condensate scaffold activity / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / chromosome, telomeric region / ribonucleoprotein complex / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
hnRNP A2/B1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterogeneous nuclear ribonucleoproteins A2/B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsAbula, A. / Liu, Y. / Guo, H. / Li, T. / Ji, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Insight Into hnRNP A2/B1 Homodimerization and DNA Recognition.
Authors: Liu, Y. / Abula, A. / Xiao, H. / Guo, H. / Li, T. / Zheng, L. / Chen, B. / Nguyen, H.C. / Ji, X.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoproteins A2/B1
B: Heterogeneous nuclear ribonucleoproteins A2/B1
C: Heterogeneous nuclear ribonucleoproteins A2/B1
D: Heterogeneous nuclear ribonucleoproteins A2/B1
E: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
F: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
G: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
H: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)97,2318
Polymers97,2318
Non-polymers00
Water17,384965
1
A: Heterogeneous nuclear ribonucleoproteins A2/B1
C: Heterogeneous nuclear ribonucleoproteins A2/B1
E: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
G: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,6154
Polymers48,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterogeneous nuclear ribonucleoproteins A2/B1
D: Heterogeneous nuclear ribonucleoproteins A2/B1
F: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
H: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,6154
Polymers48,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.190, 101.620, 111.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Heterogeneous nuclear ribonucleoproteins A2/B1 / hnRNP A2/B1


Mass: 20534.172 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 15-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA2B1, HNRPA2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22626
#2: DNA chain
DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 3773.462 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 965 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM LiCl, 0.1M HEPEs pH 7.0 , 20 % (w/v) polyethylene glycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.62→38.1 Å / Num. obs: 118490 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.558 / Mean I/σ(I) obs: 2 / Num. unique obs: 8688 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1Q

1u1q


Resolution: 1.62→33.027 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 2000 1.69 %
Rwork0.1632 116385 -
obs0.1636 118385 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.21 Å2 / Biso mean: 33.1193 Å2 / Biso min: 11.85 Å2
Refinement stepCycle: final / Resolution: 1.62→33.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 1016 0 965 7761
Biso mean---37.63 -
Num. residues----764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157036
X-RAY DIFFRACTIONf_angle_d1.3319664
X-RAY DIFFRACTIONf_chiral_restr0.0741012
X-RAY DIFFRACTIONf_plane_restr0.0091092
X-RAY DIFFRACTIONf_dihedral_angle_d19.854028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.62-1.66050.29911410.27048231
1.6605-1.70540.28591420.2428209
1.7054-1.75560.2581410.22928264
1.7556-1.81230.23061420.22178209
1.8123-1.8770.22881410.19798241
1.877-1.95220.18511420.16988278
1.9522-2.0410.19651410.16968239
2.041-2.14860.20911430.16438271
2.1486-2.28320.18741430.16288294
2.2832-2.45940.19241420.16338303
2.4594-2.70680.17791430.16628332
2.7068-3.09830.20581440.16818382
3.0983-3.90250.16371460.14678438
3.9025-100.1491490.14058694
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)
10.0271-0.02790.02490.0201-0.02350.01410.1324-0.1372-0.0416-0.0394-0.1448-0.02830.0298-0.1772-00.16060.01560.00520.1769-0.03540.1404-12.7192-1.5219.2325
20.1021-0.02720.10490.24260.00320.2023-0.0468-0.3363-0.18770.38740.05110.05070.5332-0.04390.01640.3064-0.05250.03450.25070.05440.1861-11.1826-15.891726.1559
30.1617-0.04660.09380.0434-0.01170.04620.1564-0.134-0.1642-0.0348-0.12320.17180.1187-0.243100.2482-0.0599-0.00170.2252-0.02010.2268-14.8655-16.600216.2443
40.36190.11370.06090.15880.06140.12510.0273-0.14870.00170.1433-0.0344-0.03310.0716-0.0929-00.19010.0005-0.01440.19160.00620.1327-6.6897-7.174622.023
50.0189-0.0243-0.00130.0676-0.00920.00830.1130.1702-0.10740.1123-0.1375-0.10930.0323-0.00640.00010.14090.0019-0.01010.1929-0.01230.19620.3213-3.25778.6431
60.04620.0266-0.05040.01890.00820.10060.01770.03240.11060.0998-0.1293-0.2505-0.0969-0.0003-0.00190.1942-0.0198-0.04940.12280.02060.24499.432215.052611.0278
70.2146-0.12990.30110.9415-0.34110.46110.0613-0.37950.27940.480.0169-0.1108-0.44010.10870.1170.3274-0.0313-0.06510.2502-0.08480.24987.456513.57321.7222
80.04290.0838-0.01470.18370.15810.18420.0309-0.1390.04730.11320.0767-0.2714-0.21190.12110.00250.2128-0.0812-0.03120.1870.0180.298516.767211.895310.8264
90.09380.0955-0.01270.19130.15220.16360.0408-0.10330.09650.0882-0.0475-0.0176-0.1137-0.0394-00.17730.0059-0.03580.1656-0.00180.2012.78277.435716.0267
100.0586-0.0323-0.05260.08190.08390.0730.00610.1976-0.0458-0.1303-0.0834-0.12570.0186-0.3661-0.00050.17060.0276-0.01290.21090.00340.18675.72975.63276.2851
110.12560.0178-0.01540.0191-0.02330.08650.04640.0764-0.08830.0107-0.04630.07250.0486-0.079900.1673-0.01790.00110.18390.01180.1984-26.2625-8.53663.5252
120.1556-0.07230.01620.0405-0.00620.10.07580.04460.23830.19330.02650.2175-0.0817-0.3909-00.18610.03890.04590.2799-0.00650.2519-37.8572.44137.0242
130.2780.1864-0.15010.2842-0.06910.77940.06050.07870.0890.0858-0.03540.0566-0.0288-0.197300.14940.001-0.00330.18050.01560.182-30.3955-0.06833.8974
140.02610.0489-0.00860.0936-0.05380.0388-0.0140.02640.35760.0161-0.21410.1780.11820.17030.00030.1745-0.00430.00420.2610.04360.2214-18.01880.391-7.4541
150.11520.0271-0.05230.09780.05510.0940.18050.20120.0696-0.2337-0.23710.02210.08740.15380.00010.26590.0794-0.03240.30850.03770.1497-16.258-15.6741-21.5195
160.0554-0.036-0.01960.0606-0.01560.0273-0.02780.04-0.2344-0.0295-0.00710.47750.2841-0.1716-0.00190.2448-0.0335-0.06850.27070.02850.2413-26.6685-17.4715-18.6722
170.11840.16350.02230.24350.01140.02620.01140.07630.1226-0.2128-0.00730.09960.13260.1141-0.02470.24220.06470.00760.40430.06420.1312-17.6497-11.2967-28.0848
180.032-0.0245-0.00370.0847-0.05010.02640.03620.07190.00930.007-0.07340.02940.0169-0.0191-0.01230.20180.0164-0.01740.26330.03530.1575-24.5707-7.5724-13.6072
190.0102-0.01610.0050.0213-0.00460.01180.1092-0.1285-0.0478-0.03720.0017-0.00080.1433-0.1976-0.00010.26890.0212-0.03060.26710.05720.2315-17.0866-18.5118-11.6147
200.04470.01710.05260.0883-0.03550.06790.0599-0.10240.12990.0005-0.3001-0.08820.06630.4259-0.0160.1627-0.0284-0.04970.28780.05490.2478-14.4005-5.0967-14.658
210.5488-0.0481-0.16380.5721-0.31830.7252-0.05830.1305-0.0302-0.2592-0.1-0.2941-0.05170.1688-0.23860.19870.00350.09340.19480.04970.259119.5504-2.8526-15.3572
220.61110.23290.12170.96860.06120.55520.03560.0806-0.0035-0.0412-0.0332-0.12370.0183-0.07210.00410.16890.02620.02650.12230.01170.16581.4933-21.2649-5.711
230.0559-0.0187-0.06860.03740.01290.08760.04390.01440.0353-0.0130.0799-0.199-0.148-0.162500.2556-0.0017-0.03860.2646-0.01230.21544.805815.408-19.5591
240.1253-0.3014-0.01190.8298-0.00290.02960.01340.16870.0132-0.24130.0318-0.4063-0.1619-0.54820.01110.2803-0.0272-0.00170.32660.0210.162-1.153515.631-34.5954
25-0.0189-0.00570.00060.08230.04380.2142-0.06360.10280.1043-0.26840.0236-0.30770.1297-0.18570.00020.3217-0.07850.00580.2614-0.01910.20920.71875.6902-31.4441
260.02980.0426-0.05520.027-0.04350.16180.01160.0576-0.03950.2526-0.0122-0.166-0.1221-0.22150.00010.30950.0359-0.03840.21950.00210.1931.945519.9615-23.9016
270.3381-0.1164-0.14570.0370.02940.0597-0.13610.2142-0.04150.04940.0375-0.1835-0.0634-0.4535-0.02410.19680.0895-0.03840.37380.04310.0913-5.591514.8488-24.0773
280.05850.04280.00780.04680.02620.0081-0.2006-0.28650.0111-0.05570.03180.0332-0.037-0.08980.00020.2190.0599-0.01840.2618-0.00270.2258-8.928910.0259-11.9898
290.0817-0.0186-0.05450.04810.02140.0447-0.2214-0.4075-0.27610.16840.20050.1797-0.1831-0.31620.00070.28440.1355-0.02390.253-0.01120.2563-9.253824.37153.7914
300.0553-0.00330.03860.03010.03030.0552-0.1237-0.13610.4896-0.01280.1501-0.471-0.2070.0696-0.00410.2660.0374-0.04590.15740.00470.409-6.025130.8789-4.1716
310.03710.0364-0.02260.1410.05160.2174-0.007-0.0939-0.10830.03410.05160.2917-0.18390.05920.00070.27980.12180.06830.25940.07070.3143-17.2274263.3696
320.1156-0.0824-0.04370.04790.02860.03740.2017-0.0757-0.1979-0.07070.06710.2835-0.05990.14860.0040.22770.0982-0.03220.23880.02650.2588-12.900823.5866-5.9809
330.07-0.0821-0.00520.10930.03960.05810.0622-0.0650.0838-0.1739-0.1071-0.2742-0.1525-0.14380.00080.21130.0641-0.03840.2215-0.01680.2468-2.362920.9719-6.4459
340.02440.0244-0.0120.0356-0.01130.0003-0.108-0.1568-0.36220.08030.1644-0.14440.24110.0194-0.00090.24870.0481-0.02510.20320.0350.3453-10.764914.363-2.1706
350.01670.11560.10480.24990.26730.35540.01180.02390.01580.0458-0.0790.01530.1164-0.13570.00010.16940.00760.0040.1481-0.00090.1682-7.4438-16.41887.6504
360.0513-0.02220.030.1435-0.13690.05550.0453-0.04670.35580.1991-0.01180.14620.1203-0.0651-0.00610.11850.0230.01040.15050.02620.2712-20.404410.43554.768
370.0045-0.0375-0.0150.07390.11320.3046-0.01830.02030.0995-0.10110.0149-0.1679-0.14670.141-00.1795-0.004-0.00990.16310.02730.237113.98595.7779-3.1154
380.1847-0.0786-0.07280.16960.004-0.012-0.1941-0.023-0.0847-0.26490.3599-0.2142-0.0219-0.03840.05750.2161-0.0158-0.01430.27890.08620.1517-6.5814-0.6251-24.36
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 26 )A15 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 44 )A27 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 63 )A45 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 101 )A64 - 101
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 112 )A102 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 124 )A113 - 124
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 135 )A125 - 135
8X-RAY DIFFRACTION8chain 'A' and (resid 136 through 154 )A136 - 154
9X-RAY DIFFRACTION9chain 'A' and (resid 155 through 179 )A155 - 179
10X-RAY DIFFRACTION10chain 'A' and (resid 180 through 193 )A180 - 193
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 26 )B15 - 26
12X-RAY DIFFRACTION12chain 'B' and (resid 27 through 44 )B27 - 44
13X-RAY DIFFRACTION13chain 'B' and (resid 45 through 101 )B45 - 101
14X-RAY DIFFRACTION14chain 'B' and (resid 102 through 112 )B102 - 112
15X-RAY DIFFRACTION15chain 'B' and (resid 113 through 124 )B113 - 124
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 135 )B125 - 135
17X-RAY DIFFRACTION17chain 'B' and (resid 136 through 154 )B136 - 154
18X-RAY DIFFRACTION18chain 'B' and (resid 155 through 171 )B155 - 171
19X-RAY DIFFRACTION19chain 'B' and (resid 172 through 179 )B172 - 179
20X-RAY DIFFRACTION20chain 'B' and (resid 180 through 193 )B180 - 193
21X-RAY DIFFRACTION21chain 'C' and (resid 15 through 101 )C15 - 101
22X-RAY DIFFRACTION22chain 'C' and (resid 102 through 193 )C102 - 193
23X-RAY DIFFRACTION23chain 'D' and (resid 15 through 26 )D15 - 26
24X-RAY DIFFRACTION24chain 'D' and (resid 27 through 44 )D27 - 44
25X-RAY DIFFRACTION25chain 'D' and (resid 45 through 63 )D45 - 63
26X-RAY DIFFRACTION26chain 'D' and (resid 64 through 81 )D64 - 81
27X-RAY DIFFRACTION27chain 'D' and (resid 82 through 101 )D82 - 101
28X-RAY DIFFRACTION28chain 'D' and (resid 102 through 112 )D102 - 112
29X-RAY DIFFRACTION29chain 'D' and (resid 113 through 124 )D113 - 124
30X-RAY DIFFRACTION30chain 'D' and (resid 125 through 135 )D125 - 135
31X-RAY DIFFRACTION31chain 'D' and (resid 136 through 153 )D136 - 153
32X-RAY DIFFRACTION32chain 'D' and (resid 154 through 162 )D154 - 162
33X-RAY DIFFRACTION33chain 'D' and (resid 163 through 179 )D163 - 179
34X-RAY DIFFRACTION34chain 'D' and (resid 180 through 193 )D180 - 193
35X-RAY DIFFRACTION35chain 'E' and (resid 1 through 12 )E1 - 12
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 12 )F1 - 12
37X-RAY DIFFRACTION37chain 'G' and (resid 1 through 12 )G1 - 12
38X-RAY DIFFRACTION38chain 'H' and (resid 1 through 12 )H1 - 12

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