[English] 日本語
Yorodumi
- PDB-5t7v: Methicillin Resistant, Linezolid resistant Staphylococcus aureus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t7v
TitleMethicillin Resistant, Linezolid resistant Staphylococcus aureus 70S ribosome (delta S145 uL3)
Components
  • (30S ribosomal protein ...) x 12
  • (50S ribosomal protein ...) x 26
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNA
KeywordsRIBOSOME / 70S ribosome / methicillin resistant / linezolid resistant / cryoEM
Function / homology
Function and homology information


large ribosomal subunit / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding ...large ribosomal subunit / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type ...Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L20 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal L32p protein family / Ribosomal protein S12, bacterial-type / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein L2 signature. / : / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / : / Ribosomal protein S5 signature. / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein S5, N-terminal domain
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / 50S ribosomal protein L6 / 50S ribosomal protein L27 / : / : / : / : / 50S ribosomal protein L32 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL30
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBelousoff, M.J. / Lithgow, T. / Eyal, Z. / Yonath, A. / Radjainia, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
NHMRC1092262 Australia
CitationJournal: mBio / Year: 2017
Title: Structural Basis for Linezolid Binding Site Rearrangement in the Ribosome.
Authors: Matthew J Belousoff / Zohar Eyal / Mazdak Radjainia / Tofayel Ahmed / Rebecca S Bamert / Donna Matzov / Anat Bashan / Ella Zimmerman / Satabdi Mishra / David Cameron / Hans Elmlund / Anton Y ...Authors: Matthew J Belousoff / Zohar Eyal / Mazdak Radjainia / Tofayel Ahmed / Rebecca S Bamert / Donna Matzov / Anat Bashan / Ella Zimmerman / Satabdi Mishra / David Cameron / Hans Elmlund / Anton Y Peleg / Shashi Bhushan / Trevor Lithgow / Ada Yonath /
Abstract: An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of This high-resolution ...An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Experimental preparation / Category: em_image_scans / em_sample_support / Item: _em_sample_support.grid_type
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8369
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S ribosomal RNA
S1: 30S ribosomal protein S10
S2: 30S ribosomal protein S11
S3: 30S ribosomal protein S12
S6: 30S ribosomal protein S15
S7: 30S ribosomal protein S16
S8: 30S ribosomal protein S17
S9: 30S ribosomal protein S18
SA: 30S ribosomal protein S20
SC: 30S ribosomal protein S4
SD: 30S ribosomal protein S5
SE: 30S ribosomal protein S6
SF: 30S ribosomal protein S8
B: 23S ribosomal RNA
C: 5S ribosomal RNA
L1: 50S ribosomal protein L19
L2: 50S ribosomal protein L2
L3: 50S ribosomal protein L20
L4: 50S ribosomal protein L21
L5: 50S ribosomal protein L22
L6: 50S ribosomal protein L23
L7: 50S ribosomal protein L24
L8: 50S ribosomal protein L25
L9: 50S ribosomal protein L27
LA: 50S ribosomal protein L28
LB: 50S ribosomal protein L29
LC: 50S ribosomal protein L3
LD: 50S ribosomal protein L30
LE: 50S ribosomal protein L32
LF: 50S ribosomal protein L33
LG: 50S ribosomal protein L34
LH: 50S ribosomal protein L35
LI: 50S ribosomal protein L36
LJ: 50S ribosomal protein L4
LL: 50S ribosomal protein L6
LM: 50S ribosomal protein L13
LN: 50S ribosomal protein L14
LO: 50S ribosomal protein L15
LP: 50S ribosomal protein L16
LQ: 50S ribosomal protein L17
LR: 50S ribosomal protein L18
D: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,971,15359
Polymers1,970,74042
Non-polymers41317
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area199360 Å2
ΔGint-1896 kcal/mol
Surface area736430 Å2
MethodPISA

-
Components

-
RNA chain , 4 types, 4 molecules ABCD

#1: RNA chain 16S ribosomal RNA


Mass: 500520.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1102759359
#14: RNA chain 23S ribosomal RNA


Mass: 945427.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1015534143
#15: RNA chain 5S ribosomal RNA


Mass: 36652.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1043615627
#42: RNA chain E-site tRNA


Mass: 23851.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria)

-
30S ribosomal protein ... , 12 types, 12 molecules S1S2S3S6S7S8S9SASCSDSESF

#2: Protein 30S ribosomal protein S10


Mass: 9214.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0H2K0A0
#3: Protein 30S ribosomal protein S11


Mass: 12146.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKD6
#4: Protein 30S ribosomal protein S12


Mass: 15131.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U1C6
#5: Protein 30S ribosomal protein S15


Mass: 10345.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6H8
#6: Protein 30S ribosomal protein S16


Mass: 8455.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1K8TAS5
#7: Protein 30S ribosomal protein S17


Mass: 9623.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VLD5
#8: Protein 30S ribosomal protein S18


Mass: 6533.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1D4K9U8
#9: Protein 30S ribosomal protein S20


Mass: 8295.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1K8EL93
#10: Protein 30S ribosomal protein S4


Mass: 22763.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TVK2
#11: Protein 30S ribosomal protein S5


Mass: 16245.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUC9
#12: Protein 30S ribosomal protein S6


Mass: 10864.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TPC6
#13: Protein 30S ribosomal protein S8


Mass: 14536.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8T8

+
50S ribosomal protein ... , 26 types, 26 molecules L1L2L3L4L5L6L7L8L9LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLR

#16: Protein 50S ribosomal protein L19


Mass: 13003.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UVB6
#17: Protein 50S ribosomal protein L2


Mass: 29956.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: B3VKN3
#18: Protein 50S ribosomal protein L20


Mass: 13459.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VMP6
#19: Protein 50S ribosomal protein L21


Mass: 11168.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: D7URR3
#20: Protein 50S ribosomal protein L22


Mass: 12199.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKF9
#21: Protein 50S ribosomal protein L23


Mass: 10181.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUB4
#22: Protein 50S ribosomal protein L24


Mass: 11115.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRD5
#23: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 10348.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1K8M064
#24: Protein 50S ribosomal protein L27


Mass: 8496.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0U1N012, UniProt: A0A7U7PYN3*PLUS
#25: Protein 50S ribosomal protein L28


Mass: 6607.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077URJ8
#26: Protein 50S ribosomal protein L29


Mass: 7205.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077W1J5
#27: Protein 50S ribosomal protein L3


Mass: 23112.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U3W0
#28: Protein 50S ribosomal protein L30


Mass: 6305.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UVN7
#29: Protein 50S ribosomal protein L32


Mass: 6098.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q8DAT0
#30: Protein/peptide 50S ribosomal protein L33


Mass: 5655.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UXT4
#31: Protein/peptide 50S ribosomal protein L34


Mass: 5323.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YZB6
#32: Protein 50S ribosomal protein L35


Mass: 7461.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UL47
#33: Protein/peptide 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8
#34: Protein 50S ribosomal protein L4


Mass: 22179.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRC7
#35: Protein 50S ribosomal protein L6


Mass: 19414.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0U1MRH3
#36: Protein 50S ribosomal protein L13


Mass: 16171.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUE6
#37: Protein 50S ribosomal protein L14


Mass: 13044.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UUA0
#38: Protein 50S ribosomal protein L15


Mass: 15384.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGA7
#39: Protein 50S ribosomal protein L16


Mass: 15486.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V4G0
#40: Protein 50S ribosomal protein L17


Mass: 13640.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UG91
#41: Protein 50S ribosomal protein L18


Mass: 12792.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRE0

-
Non-polymers , 1 types, 17 molecules

#43: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Clinical isolate Linezolid resistant MRSA 70S ribosome
Type: RIBOSOME / Entity ID: #1-#42 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: (dev_2429: phenix.real_space_refine) / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80500 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

+
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://pdbjlvh1.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