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- PDB-3md1: Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Bindi... -

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Entry
Database: PDB / ID: 3md1
TitleCrystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)
ComponentsNuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
KeywordsRNA BINDING PROTEIN / RRM / RBD / RNP / poly(U) binding / Pub1 / Nucleus / RNA-binding
Function / homology
Function and homology information


poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to glucose starvation / translational termination / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic stress granule / ribosome binding / mRNA binding ...poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to glucose starvation / translational termination / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic stress granule / ribosome binding / mRNA binding / nucleus / cytoplasm
Similarity search - Function
: / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 ...: / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, H. / Shi, H. / Li, Y. / Cui, Y. / Niu, L. / Teng, M.
CitationJournal: To be published
Title: Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)
Authors: Li, H. / Shi, H. / Li, Y. / Cui, Y. / Niu, L. / Teng, M.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9554
Polymers18,7712
Non-polymers1842
Water2,720151
1
A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4772
Polymers9,3851
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4772
Polymers9,3851
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4326
Polymers28,1563
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area2860 Å2
ΔGint-24 kcal/mol
Surface area12560 Å2
MethodPISA
4
B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4326
Polymers28,1563
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.661, 72.661, 81.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 / ARS consensus-binding protein ACBP-60 / Poly uridylate-binding protein / Poly(U)-binding protein


Mass: 9385.273 Da / Num. of mol.: 2 / Fragment: second RRM domain / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32588
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% (w/v) polyethylene glycol 4000 (PEG4000), 0.1 M sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20050 / Redundancy: 5.7 % / Biso Wilson estimate: 13.1 Å2
Reflection shellResolution: 1.6→50 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Num. unique all: 20050

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CVJ
Resolution: 1.6→49.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.52 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22051 1083 5.1 %RANDOM
Rwork0.19812 ---
obs0.19929 20050 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 12 151 1443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9111819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52824.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17615207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.169158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021074
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5841.5816
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03321303
X-RAY DIFFRACTIONr_scbond_it1.563529
X-RAY DIFFRACTIONr_scangle_it2.2144.5516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 77 -
Rwork0.33 1380 -
obs--91.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.48720.31580.33892.59861.16013.241-0.26510.19520.2131-0.15090.0399-0.0647-0.19760.18520.22520.08640.0155-0.03960.10210.0280.1254-20.110314.1332-3.309
20.8209-0.35331.12470.47690.45484.2553-0.054-0.0483-0.0990.0608-0.02060.11330.0312-0.18780.07460.07160.03650.03530.09220.03040.1467-33.56254.46661.1461
35.82221.5616-0.85440.5450.42174.0778-0.1209-0.41230.1447-0.0005-0.10610.099-0.1118-0.37820.2270.20160.18790.06780.22540.01650.0695-35.448611.29927.0605
45.11941.51281.26112.2794-1.77862.8369-0.027-0.1110.11050.40530.0620.0999-0.4964-0.1112-0.03510.17040.0964-0.00720.0895-0.02340.05-27.565912.91798.351
55.50831.3379-0.71069.6517-0.55248.509-0.1842-0.35170.12990.32720.0491-0.1262-0.14730.02160.13510.16290.039-0.10570.0462-0.02610.0697-19.049514.244810.4035
69.19172.78082.23083.11841.07880.6154-0.21960.03830.22330.33080.15670.09480.00550.02220.06290.17230.0645-0.03870.0957-0.02290.0845-26.358217.76063.5463
712.7364-5.79425.38997.7122-1.00683.7551-0.03860.2457-0.0787-0.06230.01570.0299-0.15110.06820.02290.07950.0170.02150.06970.03180.104-40.102114.8388-6.3817
88.3803-4.04933.88964.4281-2.58582.026-0.0519-0.1061-0.2822-0.14070.14690.2060.0339-0.029-0.0950.09490.04190.01710.11160.03640.1388-37.84269.8303-4.7023
913.99254.17118.01663.39622.70154.6381-0.1860.02860.23030.01180.05510.0681-0.09910.02120.13090.10140.0178-0.01690.08760.00070.1034-23.544814.63280.2248
101.26391.3628-2.019310.9640.46683.9763-0.0082-0.03950.0723-0.1010.2444-0.5484-0.04040.157-0.23620.0733-0.0071-0.1120.09620.0160.2576-12.529114.74191.4455
116.16892.8398-0.3433.0185-1.67231.5086-0.23390.20360.09670.09080.1381-0.225-0.0026-0.04370.09590.19970.0387-0.120.0855-0.0080.1721-16.07715.97983.3461
1215.0889-2.1527-1.74662.53370.81021.89270.085-0.525-0.29120.1982-0.0337-0.0258-0.1332-0.0104-0.05130.11860.03550.0030.08480.03020.0503-26.7781.14146.4137
138.76051.8075-2.43861.32460.1981.2079-0.13040.0984-0.1580.13670.05890.01050.1679-0.04210.07150.11720.01880.01820.12280.03610.0879-29.05550.0792.3485
143.53171.02930.65176.5945-3.2722.0602-0.15920.2629-0.0165-0.2406-0.0514-0.39330.14750.13880.21060.14250.03390.01960.12910.02110.0888-19.72368.1822-4.5691
152.16880.0257-2.15417.18735.71226.7246-0.19170.01820.0121-0.14330.14060.1752-0.00750.16640.05110.1716-0.02330.01690.1275-0.03970.0973-26.95088.2746-15.565
163.9248-0.8672.1056.8846-0.7762.81020.1118-0.0572-0.3062-0.33860.052-0.27770.3175-0.2147-0.16390.0687-0.0595-0.00270.10320.04120.1323-14.5621-9.954810.3377
170.3439-0.0295-0.9180.00280.06024.50510.0241-0.05770.08020.00120.0229-0.0105-0.2973-0.4375-0.0470.06470.0657-0.01940.189-0.03440.1174-15.42126.370714.653
180.46841.3518-0.58266.63650.2022.0730.1034-0.1343-0.03750.1343-0.0902-0.2084-0.34380.2846-0.01320.10480.0234-0.05480.2695-0.04480.0806-8.21884.490520.1553
190.2169-0.727-0.09382.979-0.71782.8775-0.0726-0.10260.02410.31080.1783-0.1081-0.1056-0.012-0.10580.03370.0057-0.01590.25640.04170.0635-11.713-2.913221.9768
2011.6673-3.70060.38439.08331.91580.66260.0104-0.9523-0.6001-0.02520.2163-0.2762-0.0461-0.2161-0.22660.0590.00730.00240.33280.19660.1384-14.9527-10.435824.2739
211.98870.62920.74445.1699-2.84922.19760.0019-0.4244-0.2428-0.2783-0.0443-0.25110.15-0.18680.04230.0558-0.0213-0.01550.16810.05150.1308-8.3584-8.024617.9819
227.21945.684-4.28595.5561-4.67114.1006-0.10610.0457-0.1962-0.01760.0549-0.0903-0.0199-0.0510.05130.05270.0158-0.01380.0751-0.02580.1587-4.49024.54788.9554
2314.28441.6666-1.39620.2418-0.47863.7725-0.12150.24960.7969-0.04030.07320.1172-0.1579-0.12880.04840.1182-0.0166-0.03250.06720.01570.1997-4.85469.53067.4508
242.49130.64430.353710.9488-4.91032.3712-0.048-0.24250.0531-0.11110.0321-0.04910.0447-0.09390.01590.0691-0.009-0.00260.12670.01380.1071-12.0895-1.963211.5356
2530.073-6.04850.21753.5231-3.78456.0694-0.4405-0.2658-1.467-0.20430.40330.31890.5034-0.4170.03720.0956-0.0962-0.04120.16020.13790.2409-16.9-15.937115.7853
262.40660.3263-1.5025.57993.86153.94160.0569-0.1081-0.1432-0.1452-0.16340.0365-0.1147-0.12390.10650.0196-0.0527-0.04080.23370.16650.1348-22.6045-10.81316.1132
271.0221-0.05351.09415.15370.12966.75520.01510.0370.0230.2336-0.09160.1431-0.0047-0.3060.07650.01420.01630.01290.20590.08130.075-24.658-2.598119.0404
283.65212.12681.95324.84670.61652.97770.1748-0.49750.22940.1324-0.00280.1811-0.2975-0.418-0.1720.13110.06020.04530.2006-0.03190.0842-19.79397.173419.5885
294.183-3.03220.946710.87796.28596.44470.0985-0.0467-0.2519-0.422-0.00420.2546-0.3201-0.4652-0.09430.06260.00940.00120.27620.07560.069-20.1522-3.963110.2437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A161 - 165
2X-RAY DIFFRACTION2A166 - 171
3X-RAY DIFFRACTION3A172 - 177
4X-RAY DIFFRACTION4A178 - 182
5X-RAY DIFFRACTION5A183 - 187
6X-RAY DIFFRACTION6A188 - 193
7X-RAY DIFFRACTION7A194 - 198
8X-RAY DIFFRACTION8A199 - 205
9X-RAY DIFFRACTION9A206 - 210
10X-RAY DIFFRACTION10A211 - 216
11X-RAY DIFFRACTION11A217 - 223
12X-RAY DIFFRACTION12A224 - 229
13X-RAY DIFFRACTION13A230 - 234
14X-RAY DIFFRACTION14A235 - 238
15X-RAY DIFFRACTION15A239 - 243
16X-RAY DIFFRACTION16B161 - 165
17X-RAY DIFFRACTION17B166 - 171
18X-RAY DIFFRACTION18B172 - 177
19X-RAY DIFFRACTION19B178 - 182
20X-RAY DIFFRACTION20B183 - 187
21X-RAY DIFFRACTION21B188 - 192
22X-RAY DIFFRACTION22B193 - 197
23X-RAY DIFFRACTION23B198 - 203
24X-RAY DIFFRACTION24B204 - 209
25X-RAY DIFFRACTION25B210 - 215
26X-RAY DIFFRACTION26B216 - 220
27X-RAY DIFFRACTION27B221 - 226
28X-RAY DIFFRACTION28B227 - 232
29X-RAY DIFFRACTION29B233 - 239

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