[English] 日本語
Yorodumi
- EMDB-52073: Human LINE-1 ORF2p target-primed reverse transcription complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52073
TitleHuman LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved
Map dataLINE-1 ORF2p TPRT Complex EN Resolved Sharpened Map
Sample
  • Complex: Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved
    • Complex: ORF2p
      • Protein or peptide: LINE-1 retrotransposable element ORF2 protein
    • Complex: Target DNA
      • DNA: Target DNA strand 1
      • DNA: Target DNA strand 2
      • DNA: Target DNA strand 3
      • DNA: Target DNA strand 4
    • RNA: Template P(A)30 RNA
    • DNA: Unassigned Nucleic Acid
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
KeywordsLINE-1 / L1 / ORF2p / Reverse transcriptase / endonuclease / DNA / RNA / RNA BINDING PROTEIN
Function / homology
Function and homology information


retrotransposition / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / nucleic acid metabolic process / Postmitotic nuclear pore complex (NPC) reformation / septin ring ...retrotransposition / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / nucleic acid metabolic process / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / type II site-specific deoxyribonuclease activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / SUMOylation of chromatin organization proteins / detection of maltose stimulus / maltose transport complex / carbohydrate transport / ubiquitin-like protein ligase binding / protein sumoylation / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / RNA-directed DNA polymerase activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / condensed nuclear chromosome / cell chemotaxis / protein tag activity / RNA-directed DNA polymerase / telomerase activity / outer membrane-bounded periplasmic space / DNA recombination / periplasmic space / DNA damage response / RNA binding / identical protein binding / nucleus / membrane / metal ion binding
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
LINE-1 retrotransposable element ORF2 protein / Maltose/maltodextrin-binding periplasmic protein / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGhanim GE / Hu H / Nguyen THD
Funding support United Kingdom, United States, European Union, 3 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
Jane Coffin Childs (JCC) Fund United States
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Science / Year: 2025
Title: Structural mechanism of LINE-1 target-primed reverse transcription.
Authors: George E Ghanim / Hongmiao Hu / Jerome Boulanger / Thi Hoang Duong Nguyen /
Abstract: Long interspersed element-1 (LINE-1) retrotransposons are the only active autonomous transposable elements in humans. They propagate by reverse transcribing their mRNA into new genomic locations by a ...Long interspersed element-1 (LINE-1) retrotransposons are the only active autonomous transposable elements in humans. They propagate by reverse transcribing their mRNA into new genomic locations by a process called target-primed reverse transcription (TPRT). Here, we present four cryo-electron microscopy structures of the human LINE-1 TPRT complex, revealing the conformational dynamics of ORF2p and its extensive remodeling of the target DNA for TPRT initiation. We observe nicking of the DNA second strand during reverse transcription of the first strand. Structure prediction identifies high-confidence binding sites for LINE-1-associated factors, namely PCNA and PABPC1, on ORF2p. Together with our structural data, this suggests a mechanism by which these factors regulate retrotransposition and proposes a model for TPRT that accounts for retrotransposition outcomes observed in cells.
History
DepositionNov 12, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52073.png

Downloads & links

-
Map

FileDownload / File: emd_52073.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLINE-1 ORF2p TPRT Complex EN Resolved Sharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 280 pix.
= 267.4 Å		0.96 Å/pix.
x 280 pix.
= 267.4 Å		0.96 Å/pix.
x 280 pix.
= 267.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.023121584 - 0.044023164
Average (Standard dev.)0.00003786686 (±0.0011610179)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 267.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52073_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: LINE-1 ORF2p TPRT Complex EN Resolved Map

Fileemd_52073_additional_1.map
AnnotationLINE-1 ORF2p TPRT Complex EN Resolved Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: LINE-1 ORF2p TPRT Complex EN Resolved half-map 1

Fileemd_52073_half_map_1.map
AnnotationLINE-1 ORF2p TPRT Complex EN Resolved half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: LINE-1 ORF2p TPRT Complex EN Resolved half-map 2

Fileemd_52073_half_map_2.map
AnnotationLINE-1 ORF2p TPRT Complex EN Resolved half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Human LINE-1 ORF2p target-primed reverse transcription complex wi...

EntireName: Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved
Components
  • Complex: Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved
    • Complex: ORF2p
      • Protein or peptide: LINE-1 retrotransposable element ORF2 protein
    • Complex: Target DNA
      • DNA: Target DNA strand 1
      • DNA: Target DNA strand 2
      • DNA: Target DNA strand 3
      • DNA: Target DNA strand 4
    • RNA: Template P(A)30 RNA
    • DNA: Unassigned Nucleic Acid
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE

+
Supramolecule #1: Human LINE-1 ORF2p target-primed reverse transcription complex wi...

SupramoleculeName: Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: The human LINE-1 retrotransposon mobilizes using the encoded ORF2p protein by a mechanism called target-primed reverse transcription.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52 KDa

+
Supramolecule #2: ORF2p

SupramoleculeName: ORF2p / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: LINE-1 ORF2p protein
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Target DNA

SupramoleculeName: Target DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3, #5-#6
Details: Target DNA idealized from a de novo LINE-1 insertion into the FVIII gene
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: LINE-1 retrotransposable element ORF2 protein

MacromoleculeName: LINE-1 retrotransposable element ORF2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 206.717625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVHHHHHHHH GGSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGSEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI Y NKDLLPNP ...String:
MVHHHHHHHH GGSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGSEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI Y NKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL VD LIKNKHM NADTDYSIAE AAFNKGETAM TINGPWAWSN IDTSKVNYGV TVLPTFKGQP SKPFVGVLSA GINAASPNKE LAK EFLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELVK DPRIAATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTV DEALK DAQTNSSSNN NNNNNNNNLG SDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQ GKEM DSLTFLYDGI EIQADQTPED LDMEDNDIIE AHREQIGGMT GSTSHITILT LNINGLNSAI KRHRLASWIK SQDPSV CCI QETHLTCRDT HRLKIKGWRK IYQANGKQKK AGVAILVSDK TDFKPTKIKR DKEGHYIMVK GSIQQEELTI LNIYAPN TG APRFIKQVLS DLQRDLDSHT LIMGDFNTPL STLDRSTRQK VNKDTQELNS ALHQADLIDI YRTLHPKSTE YTFFSAPH H TYSKIDHIVG SKALLSKCKR TEIITNYLSD HSAIKLELRI KNLTQSRSTT WKLNNLLLND YWVHNEMKAE IKMFFETNE NKDTTYQNLW DAFKAVCRGK FIALNAYKRK QERSKIDTLT SQLKELEKQE QTHSKASRRQ EITKIRAELK EIETQKTLQK INESRSWFF ERINKIDRPL ARLIKKKREK NQIDTIKNDK GDITTDPTEI QTTIREYYKH LYANKLENLE EMDTFLDTYT L PRLNQEEV ESLNRPITGS EIVAIINSLP TKKSPGPDGF TAEFYQRYKE ELVPFLLKLF QSIEKEGILP NSFYEASIIL IP KPGRDTT KKENFRPISL MNIDAKILNK ILANRIQQHI KKLIHHDQVG FIPGMQGWFN IRKSINVIQH INRAKDKNHM IIS IDAEKA FDKIQQPFML KTLNKLGIDG TYFKIIRAIY DKPTANIILN GQKLEAFPLK TGTRQGCPLS PLLFNIVLEV LARA IRQEK EIKGIQLGKE EVKLSLFADD MIVYLENPIV SAQNLLKLIS NFSKVSGYKI NVQKSQAFLY TNNRQTESQI MGELP FTIA SKRIKYLGIQ LTRDVKDLFK ENYKPLLKEI KEETNKWKNI PCSWVGRINI VKMAILPKVI YRFNAIPIKL PMTFFT ELE KTTLKFIWNQ KRARIAKSIL SQKNKAGGIT LPDFKLYYKA TVTKTAWYWY QNRDIDQWNR TEPSEIMPHI YNYLIFD KP EKNKQWGKDS LFNKWCWENW LAICRKLKLD PFLTPYTKIN SRWIKDLNVK PKTIKTLEEN LGITIQDIGV GKDFMSKT P KAMATKDKID KWDLIKLKSF CTAKETTIRV NRQPTTWEKI FATYSSDKGL ISRIYNELKQ IYKKKTNNPI KKWAKDMNR HFSKEDIYAA KKHMKKCSSS LAIREMQIKT TMRYHLTPVR MAIIKKSGNN RCWRGCGEIG TLLHCWWDCK LVQPLWKSVW RFLRDLELE IPFDPAIPLL GIYPNEYKSC CYKDTCTRMF IAALFTIAKT WNQPKCPTMI DWIKKMWHIY TMEYYAAIKN D EFISFVGT WMKLETIILS KLSQEQKTKH RIFSLIGGN

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Ubiquitin-like protein SMT3, LINE-1 retrotransposable element ORF2 protein

+
Macromolecule #2: Target DNA strand 1

MacromoleculeName: Target DNA strand 1 / type: dna / ID: 2
Details: Modified from de novo LINE-1 insertion event into the FVIII gene
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.424341 KDa
SequenceString:
(DT)(DT)(DA)(DG)(DT)(DT)(DG)(DC)(DT)(DG) (DA)(DA)(DT)(DT)(DA)(DT)(DT)(DG)(DG)(DA) (DA)(DG)(DT)(DT)(DT)(DT)(DG)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

+
Macromolecule #3: Target DNA strand 2

MacromoleculeName: Target DNA strand 2 / type: dna / ID: 3
Details: Modified from de novo LINE-1 insertion event into the FVIII gene
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.144987 KDa
SequenceString:
(DA)(DA)(DA)(DC)(DA)(DA)(DA)(DA)(DC)(DT) (DT)(DC)(DC)(DA)(DA)(DT)(DA)(DA)(DT)(DT) (DC)(DA)(DG)(DC)(DA)(DA)(DC)(DT)(DA) (DA)

+
Macromolecule #5: Target DNA strand 3

MacromoleculeName: Target DNA strand 3 / type: dna / ID: 5
Details: Modified from de novo LINE-1 insertion event into the FVIII gene
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.900112 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DA)(DA)(DA)

+
Macromolecule #6: Target DNA strand 4

MacromoleculeName: Target DNA strand 4 / type: dna / ID: 6
Details: Modified from de novo LINE-1 insertion event into the FVIII gene
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.905973 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)

+
Macromolecule #7: Unassigned Nucleic Acid

MacromoleculeName: Unassigned Nucleic Acid / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.20787 KDa
SequenceString:
(DA)(DA)(DA)(DA)

+
Macromolecule #4: Template P(A)30 RNA

MacromoleculeName: Template P(A)30 RNA / type: rna / ID: 4
Details: Chemically synthesized 30 nucleotide Poly(A) sequence
Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.831217 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA

+
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #10: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: D3T
Molecular weightTheoretical: 466.169 Da
Chemical component information

ChemComp-23T:
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
500.0 mMCH3CO2Kpotassium acetate
1.5 mMMg(CH3COO)2magnesium acetate
10.0 uMZn(CH3COO)2zinc acetate
1.0 mMC4H10O2S2DTT
0.5 mMC7H7FO2SPMSF
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 2 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average exposure time: 5.82 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 22.0 µm / Nominal defocus min: 8.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsAll images were processed using RELION5.0 and CryoSPARC 4.5.3
Particle selectionNumber selected: 4568277
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 121941
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Chain ID: A / Chain - Residue range: 1-1275 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: Initial model was an alphaFold 2 prediction and was rebuilt into the density.
Output model

PDB-9hdr:
Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved

+
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