[English] 日本語
Yorodumi
- PDB-4pjo: Minimal U1 snRNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pjo
TitleMinimal U1 snRNP
Components
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U1 small nuclear ribonucleoprotein ...) x 2
  • RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
KeywordsSPLICING / U1 snRNP / Spliceosome / Pre-mRNA splicing / Ribonucleoprotein
Function / homology
Function and homology information


negative regulation of protein refolding / regulation of ATP-dependent activity / 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 ...negative regulation of protein refolding / regulation of ATP-dependent activity / 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 / pICln-Sm protein complex / U1 snRNP binding / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / negative regulation of chaperone-mediated autophagy / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / pre-mRNA 5'-splice site binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 5'-splice site recognition / U5 snRNP / Cajal body / spliceosomal snRNP assembly / U1 snRNA binding / 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 / single-stranded RNA binding / nuclear body / nuclear speck / mRNA binding / enzyme binding / protein homodimerization activity / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1-C, C2H2-type zinc finger / U1 zinc finger / Small ribonucleoprotein associated, SmB/SmN / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small nuclear ribonucleoprotein D1 ...snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1-C, C2H2-type zinc finger / U1 zinc finger / Small ribonucleoprotein associated, SmB/SmN / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / SH3 type barrels. - #100 / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Zinc finger C2H2 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / SH3 type barrels. / Nucleotide-binding alpha-beta plait domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ETHANOL / : / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G ...ETHANOL / : / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKondo, Y. / Oubridge, C. / van Roon, A.M. / Nagai, K.
CitationJournal: Elife / Year: 2015
Title: Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Authors: Kondo, Y. / Oubridge, C. / van Roon, A.M. / Nagai, K.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Dec 20, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small nuclear ribonucleoprotein Sm D3
B: Small nuclear ribonucleoprotein-associated proteins B and B'
C: Small nuclear ribonucleoprotein Sm D1
D: Small nuclear ribonucleoprotein Sm D2
E: Small nuclear ribonucleoprotein E
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein G
K: U1 small nuclear ribonucleoprotein 70 kDa
L: U1 small nuclear ribonucleoprotein C
1: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
X: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
k: U1 small nuclear ribonucleoprotein 70 kDa
l: U1 small nuclear ribonucleoprotein C
2: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
x: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
O: Small nuclear ribonucleoprotein Sm D3
P: Small nuclear ribonucleoprotein-associated proteins B and B'
Q: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
S: Small nuclear ribonucleoprotein E
T: Small nuclear ribonucleoprotein F
U: Small nuclear ribonucleoprotein G
N: U1 small nuclear ribonucleoprotein 70 kDa
M: U1 small nuclear ribonucleoprotein C
3: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
Y: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
o: Small nuclear ribonucleoprotein Sm D3
p: Small nuclear ribonucleoprotein-associated proteins B and B'
q: Small nuclear ribonucleoprotein Sm D1
r: Small nuclear ribonucleoprotein Sm D2
s: Small nuclear ribonucleoprotein E
t: Small nuclear ribonucleoprotein F
u: Small nuclear ribonucleoprotein G
n: U1 small nuclear ribonucleoprotein 70 kDa
m: U1 small nuclear ribonucleoprotein C
4: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
y: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)453,81679
Polymers452,17944
Non-polymers1,63735
Water86548
1
A: Small nuclear ribonucleoprotein Sm D3
B: Small nuclear ribonucleoprotein-associated proteins B and B'
C: Small nuclear ribonucleoprotein Sm D1
D: Small nuclear ribonucleoprotein Sm D2
E: Small nuclear ribonucleoprotein E
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein G
K: U1 small nuclear ribonucleoprotein 70 kDa
L: U1 small nuclear ribonucleoprotein C
1: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
X: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,58222
Polymers113,04511
Non-polymers53711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30670 Å2
ΔGint-219 kcal/mol
Surface area35810 Å2
MethodPISA
2
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
k: U1 small nuclear ribonucleoprotein 70 kDa
l: U1 small nuclear ribonucleoprotein C
2: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
x: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,54820
Polymers113,04511
Non-polymers5039
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29690 Å2
ΔGint-164 kcal/mol
Surface area35020 Å2
MethodPISA
3
O: Small nuclear ribonucleoprotein Sm D3
P: Small nuclear ribonucleoprotein-associated proteins B and B'
Q: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
S: Small nuclear ribonucleoprotein E
T: Small nuclear ribonucleoprotein F
U: Small nuclear ribonucleoprotein G
N: U1 small nuclear ribonucleoprotein 70 kDa
M: U1 small nuclear ribonucleoprotein C
3: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
Y: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,32519
Polymers113,04511
Non-polymers2808
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28250 Å2
ΔGint-169 kcal/mol
Surface area36230 Å2
MethodPISA
4
o: Small nuclear ribonucleoprotein Sm D3
p: Small nuclear ribonucleoprotein-associated proteins B and B'
q: Small nuclear ribonucleoprotein Sm D1
r: Small nuclear ribonucleoprotein Sm D2
s: Small nuclear ribonucleoprotein E
t: Small nuclear ribonucleoprotein F
u: Small nuclear ribonucleoprotein G
n: U1 small nuclear ribonucleoprotein 70 kDa
m: U1 small nuclear ribonucleoprotein C
4: U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
y: RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,36118
Polymers113,04511
Non-polymers3167
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29160 Å2
ΔGint-177 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.359, 172.627, 256.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Small nuclear ribonucleoprotein ... , 6 types, 24 molecules AaOoCcQqDdRrEeSsFfTtGgUu

#1: Protein
Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD3 / Plasmid: pQE30 / Details (production host): Coexpressed with SmB / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 (pREP4) / References: UniProt: P62318
#3: Protein
Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 10026.635 Da / Num. of mol.: 4 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Details: Expressed as a fusion protein with the N-terminal 59 residues of U1-70k protein joined via a (Gly-Ser)3 linker to its N-terminus. This fusion protein is co-expressed with SmD2.
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Plasmid: pET / Details (production host): Coexpressed with SmD1 / Production host: Escherichia coli BL21 (DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P62314
#4: Protein
Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2 / Plasmid: pET
Details (production host): Coexpressed with 70k-SmD1 fusion protein
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P62316
#5: Protein
Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Plasmid: pET15b / Details (production host): Co-expressed with SmF and SmG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62304
#6: Protein
Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 8369.846 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Plasmid: pET15b / Details (production host): Co-expressed with SmE and SmG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62306
#7: Protein
Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Plasmid: pET15b / Details (production host): Co-expressed with SmE and SmF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62308

-
Protein , 1 types, 4 molecules BbPp

#2: Protein
Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 10911.931 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPB, COD, SNRPB1 / Plasmid: pQE30 / Details (production host): Coexpressed with SmD3 / Production host: Escherichia coli / Strain (production host): SG13009 (pREP4) / References: UniProt: P14678

-
U1 small nuclear ribonucleoprotein ... , 2 types, 8 molecules KkNnLlMm

#8: Protein
U1 small nuclear ribonucleoprotein 70 kDa / snRNP70


Mass: 6862.841 Da / Num. of mol.: 4 / Mutation: M1G
Source method: isolated from a genetically manipulated source
Details: Expressed as a fusion protein with SmD1 (1-85) joined via a (Gly-Ser)3 linker at its C-terminus. This fusion protein is co-expressed with SmD2. An N-terminal tag is cleaved by TEV protease ...Details: Expressed as a fusion protein with SmD1 (1-85) joined via a (Gly-Ser)3 linker at its C-terminus. This fusion protein is co-expressed with SmD2. An N-terminal tag is cleaved by TEV protease during purification, leaving an N-terminal Gly residue.
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1 / Plasmid: pET / Details (production host): Co-expressed with SmD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P08621
#9: Protein
U1 small nuclear ribonucleoprotein C / U1C


Mass: 7279.186 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPC / Plasmid: pET3b / Production host: Escherichia coli B (bacteria) / Strain (production host): B834 (DE3) / References: UniProt: P09234

-
RNA chain , 2 types, 8 molecules 1234XxYy

#10: RNA chain
U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.


Mass: 19575.514 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Made by in vitro transcription using T7 RNA polymerase from a linearised pUC plasmid template containing a T7 promoter followed by the template sequence.
Source: (synth.) Homo sapiens (human)
#11: RNA chain
RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')


Mass: 3200.972 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: RNA made by chemical synthesis. Sequence based on consensus human 5' splice site.
Source: (synth.) Homo sapiens (human)

-
Non-polymers , 8 types, 83 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#13: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#14: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#15: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#16: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#17: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#18: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.7 % / Description: 0.3 x 0.04 x 0.04 mm^3 rods
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Minimal U1 snRNP at 4 mg/ml in 300mM KCl, 20mM KHepes, pH 7.5, 5mM MgCl2, 1mM DTT, 0.15 mM polyamine-9 mixed 1:1 with 7% MPD, 180mM KCl, 5mM MgSO4, 50mM NaHepes pH 6.4. Streak seeded.
Temp details: Cold room

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2013
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.3→70 Å / Num. all: 80571 / Num. obs: 80571 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 172.1
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3

-
Processing

Software
NameClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y9A

2y9a
PDB Unreleased entry


Resolution: 3.3→70 Å / SU ML: 0.423 / Cross valid method: FREE R-VALUE / ESU R Free: 0.518
RfactorNum. reflection% reflectionSelection details
Rfree0.25493 3972 5 %Random selection
Rwork0.20698 ---
obs0.20943 74960 97.41 %-
Displacement parametersBiso mean: 99.241 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å20 Å20 Å2
2---0.97 Å20 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 3.3→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21796 4992 69 48 26905
LS refinement shellResolution: 3.3→3.386 Å
RfactorNum. reflection% reflection
Rfree0.347 285 5 %
Rwork0.322 5286 -
obs--93.5 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more