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- PDB-1d3b: CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP D... -

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Basic information

Entry
Database: PDB / ID: 1d3b
TitleCRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP DOMAIN AT 2.0A RESOLUTION
Components
  • PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
  • PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
KeywordsRNA BINDING PROTEIN / SNRNP / SPLICING / SM / CORE SNRNP DOMAIN / SYSTEMIC LUPUS ERYTHEMATOSUS / SLE
Function / homology
Function and homology information


U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome ...U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / enzyme binding / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / SH3 type barrels. - #100 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily ...Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / SH3 type barrels. - #100 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsKambach, C. / Walke, S. / Avis, J.M. / De La Fortelle, E. / Li, J. / Nagai, K.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
Authors: Kambach, C. / Walke, S. / Young, R. / Avis, J.M. / de la Fortelle, E. / Raker, V.A. / Luhrmann, R. / Li, J. / Nagai, K.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1999
Title: Structure and Assembly of the Spliceosomal Small Nuclear Ribonucleoprotein Particles
Authors: Kambach, C. / Walke, S. / Nagai, K.
History
DepositionDec 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
B: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
C: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
D: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
E: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
F: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
G: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
H: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
I: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
J: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
K: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
L: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,64529
Polymers113,77912
Non-polymers1,86617
Water9,980554
1
A: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
B: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5247
Polymers18,9632
Non-polymers5615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
D: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1474
Polymers18,9632
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
F: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3326
Polymers18,9632
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
H: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3395
Polymers18,9632
Non-polymers3763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
J: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2474
Polymers18,9632
Non-polymers2842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
L: PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0553
Polymers18,9632
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.350, 108.450, 110.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.222, -0.074, -0.972), (-0.969, -0.128, -0.212), (-0.108, 0.989, -0.1)100.60454, 119.10007, 19.55497
2given(0.236, -0.964, -0.123), (-0.078, -0.144, 0.986), (-0.969, -0.223, -0.109)95.25601, 4.42283, 125.72305
3given(0.074, 0.218, -0.973), (0.997, 0.076), (0.017, -0.976, -0.218)97.65822, -5.00382, 65.3895
4given(-0.078, -0.997, -0.013), (0.223, -0.005, -0.975), (0.972, -0.079, 0.223)111.13881, 96.15759, -54.73518
5given(0.955, 0.102, 0.279), (0.14, -0.982, -0.123), (0.262, 0.157, -0.952)-14.4157, 100.43752, 38.40382
6given(0.199, -0.085, -0.976), (-0.975, -0.119, -0.188), (-0.1, 0.989, -0.107)102.94312, 117.47772, 19.64391
7given(0.241, -0.961, -0.135), (-0.051, -0.151, 0.987), (-0.969, -0.231, -0.086)95.61127, 3.08204, 124.66409
8given(0.047, 0.223, -0.974), (0.999, 0.003, 0.049), (0.013, -0.975, -0.222)99.09593, -3.60911, 65.84605
9given(-0.078, -0.997, -0.003), (0.195, -0.012, -0.981), (0.978, -0.077, 0.196)110.53213, 98.6289, -53.48652
10given(0.959, 0.102, 0.264), (0.137, -0.984, -0.118), (0.247, 0.149, -0.957)-13.91041, 100.38264, 40.09717
DetailsTHE BIOLOGICALLY ACTIVE UNIT IS ONE D3B HETERODIMER, REPRESENTED BY THE PAIRS OF CHAINS A+B, C+D ETC. THE HETERODIMERS ARRANGE IN TWO HEXAMERIC RINGS WITH ALTERNATING D3 AND B SUBUNITS. THE TWO RINGS CONTACT EACH OTHER VIA A PARALLEL BETA-STRAND - BETA-STRAND INTERACTION.

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Components

#1: Protein
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3) / D3 CORE SNRNP PROTEIN


Mass: 8491.800 Da / Num. of mol.: 6 / Fragment: SM MOTIF / Mutation: S66C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: N-TERMINAL HIS6 TAG CLEAVED OFF,TRUNCATED AT POSITION 75
Cellular location: NUCLEUS / Plasmid: PQE30 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P62318
#2: Protein
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B) / B CORE SNRNP PROTEIN


Mass: 10471.370 Da / Num. of mol.: 6 / Fragment: SM MOTIF / Source method: isolated from a natural source
Details: POLYCISTRONIC COEXPRESSION VECTOR WITH SM D3. TRUNCATED AT POSITION 91.
Source: (natural) Homo sapiens (human) / Cellular location: NUCLEUS / References: UniProt: P14678
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.1 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 MNa/K phosphate1reservoir
215 %glycerol1reservoir
310 mMspermidine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Details: MIRRORS
RadiationMonochromator: SI CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2→25.2 Å / Num. obs: 89816 / % possible obs: 99.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.093 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.45 / % possible all: 98.8
Reflection
*PLUS
Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.45

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: SIDECHAINS IN REGIONS OF POORLY DEFINED DENSITY (PARTICULARLY IN LOOPS) WERE MODELLED. OCCUPANCIES HAVE BEEN BEEN ARBITRARILY SET TO 0.10.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4075 5 %RANDOM
Rwork0.213 ---
obs-86568 99.2 %-
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20 Å20 Å2
2--5.15 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7555 0 123 554 8232
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0340.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8443
X-RAY DIFFRACTIONp_mcangle_it3.8975
X-RAY DIFFRACTIONp_scbond_it4.3534
X-RAY DIFFRACTIONp_scangle_it6.0916
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1930.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2590.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1490.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.620
X-RAY DIFFRACTIONp_special_tor

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