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Entry
Database: PDB / ID: 4uer
Title40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri
Components
  • 18S RRNA18S ribosomal RNA
  • EIF1
  • EIF1AEIF1AX
  • EIF3A
  • EIF3B
  • EIF3C
  • ES1
  • ES10
  • ES12
  • ES17
  • ES19
  • ES21
  • ES24
  • ES25
  • ES26
  • ES27
  • ES28
  • ES30
  • ES31
  • ES4
  • ES6
  • ES7
  • ES8
  • RACK1Receptor for activated C kinase 1
  • US10
  • US11
  • US12
  • US13
  • US14
  • US15
  • US17
  • US19
  • US2
  • US3
  • US4
  • US5
  • US7
  • US8
  • US9
KeywordsTRANSLATION / EIF3 / TRANSLATION INITIATION
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / translation initiation factor binding / translation initiation factor activity / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / small ribosomal subunit ...eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / translation initiation factor binding / translation initiation factor activity / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus ...: / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor 3 subunit A / SUI1 domain / Eukaryotic translation initiation factor eIF2A / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / : / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S19A/S15e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 4C / ES31 / 40S ribosomal protein S0 / US3 / US4 / US5 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 4C / ES31 / 40S ribosomal protein S0 / US3 / US4 / US5 / eIF1 / US7 / US8 / US9 / ES28 / US10 / US11 / US13 / US14 / US15 / US17 / Rack1 / US19 / 40S ribosomal protein S8 / ES19 / 40S ribosomal protein S12 / ES17 / 40S ribosomal protein S4 / 40S ribosomal protein S30 / 40S ribosomal protein S6 / 40S ribosomal protein S21 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit C / 40S ribosomal protein S7 / 40S ribosomal protein S1 / 40S ribosomal protein S26 / 40S ribosomal protein S27 / ES10 / 40S ribosomal protein S25 / 40S ribosomal protein S24 / RPS23
Similarity search - Component
Biological speciesLACHANCEA KLUYVERI (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.47 Å
AuthorsAylett, C.H.S. / Boehringer, D. / Erzberger, J.P. / Schaefer, T. / Ban, N.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structure of a yeast 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex.
Authors: Christopher H S Aylett / Daniel Boehringer / Jan P Erzberger / Tanja Schaefer / Nenad Ban /
Abstract: Eukaryotic translation initiation requires cooperative assembly of a large protein complex at the 40S ribosomal subunit. We have resolved a budding yeast initiation complex by cryo-EM, allowing ...Eukaryotic translation initiation requires cooperative assembly of a large protein complex at the 40S ribosomal subunit. We have resolved a budding yeast initiation complex by cryo-EM, allowing placement of prior structures of eIF1, eIF1A, eIF3a, eIF3b and eIF3c. Our structure highlights differences in initiation-complex binding to the ribosome compared to that of mammalian eIF3, demonstrates a direct contact between eIF3j and eIF1A and reveals the network of interactions between eIF3 subunits.
History
DepositionDec 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / em_3d_fitting ...atom_site / em_3d_fitting / em_image_scans / em_software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "0A" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "0A" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
0: EIF1A
1: ES28
2: ES8
3: ES7
4: ES1
5: ES26
6: ES27
7: ES10
8: ES25
9: ES31
A: 18S RRNA
B: US2
C: US3
D: US4
E: US5
F: EIF1
G: US7
H: US8
I: US9
J: US10
K: US11
L: US12
M: US13
N: US14
O: US15
P: ES24
Q: US17
R: RACK1
S: US19
T: ES19
U: ES12
V: ES17
W: ES4
X: ES30
Y: ES6
Z: ES21
a: EIF3A
b: EIF3B
c: EIF3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,428,95543
Polymers1,428,69339
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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Protein , 38 types, 38 molecules 0123456789BCDEFGHIJKLMNOPQRSTU...

#1: Protein EIF1A / EIF1AX


Mass: 11514.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X202*PLUS
#2: Protein ES28


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X212*PLUS
#3: Protein ES8


Mass: 21147.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X221*PLUS
#4: Protein ES7


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X232*PLUS
#5: Protein ES1


Mass: 24312.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X233*PLUS
#6: Protein ES26


Mass: 11022.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X234*PLUS
#7: Protein ES27


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X235*PLUS
#8: Protein ES10


Mass: 11571.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X236*PLUS
#9: Protein ES25


Mass: 8001.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X237*PLUS
#10: Protein ES31


Mass: 7406.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X203*PLUS
#12: Protein US2


Mass: 22811.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X204*PLUS
#13: Protein US3


Mass: 24702.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X205*PLUS
#14: Protein US4


Mass: 21210.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X206*PLUS
#15: Protein US5


Mass: 23212.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X207*PLUS
#16: Protein EIF1 /


Mass: 9594.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X208*PLUS
#17: Protein US7


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X209*PLUS
#18: Protein US8


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X210*PLUS
#19: Protein US9


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X211*PLUS
#20: Protein US10


Mass: 12190.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X213*PLUS
#21: Protein US11


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X214*PLUS
#22: Protein US12


Mass: 15942.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: Q875Q2*PLUS
#23: Protein US13


Mass: 16940.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X215*PLUS
#24: Protein US14


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X216*PLUS
#25: Protein US15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X217*PLUS
#26: Protein ES24


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: Q875Q1*PLUS
#27: Protein US17


Mass: 17654.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X218*PLUS
#28: Protein RACK1 / Receptor for activated C kinase 1


Mass: 34710.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X219*PLUS
#29: Protein US19


Mass: 14155.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X220*PLUS
#30: Protein ES19


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X222*PLUS
#31: Protein ES12


Mass: 13327.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X223*PLUS
#32: Protein ES17


Mass: 13768.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X224*PLUS
#33: Protein ES4


Mass: 29338.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X225*PLUS
#34: Protein ES30


Mass: 6779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X226*PLUS
#35: Protein ES6


Mass: 25895.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X227*PLUS
#36: Protein ES21


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X228*PLUS
#37: Protein EIF3A /


Mass: 110517.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X229*PLUS
#38: Protein EIF3B /


Mass: 88241.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X230*PLUS
#39: Protein EIF3C /


Mass: 93310.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus) / References: UniProt: A0A0J9X231*PLUS

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RNA chain / Non-polymers , 2 types, 5 molecules A

#11: RNA chain 18S RRNA / 18S ribosomal RNA


Mass: 571936.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) LACHANCEA KLUYVERI (fungus)
#40: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsTHE 40S SUBUNIT IS TAKEN FROM PDBS 3U5B,3U5G AND RECHAINED TO MATCH 2XZM THE UNIPROT SC EIF3B ...THE 40S SUBUNIT IS TAKEN FROM PDBS 3U5B,3U5G AND RECHAINED TO MATCH 2XZM THE UNIPROT SC EIF3B SEQUENCE USES AN UPSTREAM START CODON THOUGHT TO BE DISFAVOURED. WE HAVE USED THE NUMBERING CORRESPONDING TO THE LATER START CODON.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LACHANCEA KLUYVERI 40S- EIF1- EIF1A-EIF3-EIF3J INITIATION COMPLEX
Type: RIBOSOME / Details: MICROGRAPHS SELECTED BY CTF
Buffer solutionName: 25 MM K-HEPES, 10 MM MGCL2, 75 MM KCL, 0.5 MM TCEP / pH: 7.6 / Details: 25 MM K-HEPES, 10 MM MGCL2, 75 MM KCL, 0.5 MM TCEP
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 75, TEMPERATURE- 120, INSTRUMENT- HOMEMADE PLUNGER, METHOD- 5 SECONDS BLOTTING BEFORE PLUNGING., DETAILS- CARBON FLOATED ON THE SAMPLE PRIOR TO ...Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 75, TEMPERATURE- 120, INSTRUMENT- HOMEMADE PLUNGER, METHOD- 5 SECONDS BLOTTING BEFORE PLUNGING., DETAILS- CARBON FLOATED ON THE SAMPLE PRIOR TO RECOVERY ONTO THE GRID AND FLASH -FREEZING.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 6, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100719 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2UCSF Chimeramodel fitting
3RELION1.23D reconstruction
CTF correctionDetails: BY IMAGE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MAXIMUM A POSTERIORI PROJECTION MATCHING / Resolution: 6.47 Å / Num. of particles: 27354 / Nominal pixel size: 1.39 Å / Actual pixel size: 1.39 Å
Details: THIS DEPOSITION DETAILS AN S. CEREVISIAE MODEL FOR THE CLOSELY RELATED L. KLUYVERI STRUCTURE. INITIAL PLACEMENT OF FOLDED DOMAINS WAS ACCORDING TO THE MASS-SPECTROMETRY MODEL IN DOMAINS WERE ...Details: THIS DEPOSITION DETAILS AN S. CEREVISIAE MODEL FOR THE CLOSELY RELATED L. KLUYVERI STRUCTURE. INITIAL PLACEMENT OF FOLDED DOMAINS WAS ACCORDING TO THE MASS-SPECTROMETRY MODEL IN DOMAINS WERE FITTED INTO CRYOEM DENSITY LOW-PASS FILTERED AT MEAN LOCAL RESOLUTION AS RIGID BODIES USING CALCULATED DENSITIES GENERATED AT THE SAME RESOLUTION. CORRELATION COEFFICIENT WAS USED AS THE TARGET FUNCTION IN CHIMERA. THE RRM DOMAIN OF EIF3B IS DEPOSITED AS CA TRACE ONLY TO INDICATE THAT ITS POSITION HAS LOWER ANGULAR CONFIDENCE BECAUSE THE DOMAIN IS EXTREMELY SMALL AND GENERATED NO DIRECT CROSS-LINKS TO THE 40S TO AID PLACEMENT. EIF3B HAS BEEN NUMBERED ACCORDING TO THE SECOND START CODON AS THIS IS THOUGHT TO BE THE PREDOMINANT FORM OF THE PROTEIN IN VIVO. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2845.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 3U5B

3u5b
PDB Unreleased entry

RefinementHighest resolution: 6.47 Å
Refinement stepCycle: LAST / Highest resolution: 6.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51480 37813 4 0 89297

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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

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