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- EMDB-11990: Cryo-EM structure of complement C4b in complex with nanobody B12 -

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Basic information

Entry
Database: EMDB / ID: EMD-11990
TitleCryo-EM structure of complement C4b in complex with nanobody B12
Map dataDeepEMhancer-postprocessed, local-sharpened cryo-EM density map of complement C4b in complex with nanobody B12.
Sample
  • Complex: Complement C4b bound to nanobody B12
    • Complex: Complement C4 beta chain
      • Protein or peptide: Complement C4 beta chain
    • Complex: Complement C4 alpha chain
      • Protein or peptide: Complement C4 alpha chain
    • Complex: Complement C4 gamma chain
      • Protein or peptide: Complement C4 gamma chain
    • Complex: Nanobody B12
      • Protein or peptide: Anti-C4b nanobody B12
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


complement component C1q complex binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...complement component C1q complex binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / inflammatory response / axon / endoplasmic reticulum lumen / innate immune response / neuronal cell body / dendrite / synapse / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement C4, MG1 domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system ...: / Complement C4, MG1 domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Lama glama (llama) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsOosterheert W / De la O Becerra KI / Gros P
Funding support Mexico, 1 items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)604718 Mexico
CitationJournal: J Immunol / Year: 2022
Title: Multifaceted Activities of Seven Nanobodies against Complement C4b.
Authors: Karla I De la O Becerra / Wout Oosterheert / Ramon M van den Bos / Katerina T Xenaki / Joseph H Lorent / Maartje Ruyken / Arie Schouten / Suzan H M Rooijakkers / Paul M P van Bergen En Henegouwen / Piet Gros /
Abstract: Cleavage of the mammalian plasma protein C4 into C4b initiates opsonization, lysis, and clearance of microbes and damaged host cells by the classical and lectin pathways of the complement system. ...Cleavage of the mammalian plasma protein C4 into C4b initiates opsonization, lysis, and clearance of microbes and damaged host cells by the classical and lectin pathways of the complement system. Dysregulated activation of C4 and other initial components of the classical pathway may cause or aggravate pathologies, such as systemic lupus erythematosus, Alzheimer disease, and schizophrenia. Modulating the activity of C4b by small-molecule or protein-based inhibitors may represent a promising therapeutic approach for preventing excessive inflammation and damage to host cells and tissue. Here, we present seven nanobodies, derived from llama () immunization, that bind to human C4b () with high affinities ranging from 3.2 nM to 14 pM. The activity of the nanobodies varies from no to complete inhibition of the classical pathway. The inhibiting nanobodies affect different steps in complement activation, in line with blocking sites for proconvertase formation, C3 substrate binding to the convertase, and regulator-mediated inactivation of C4b. For four nanobodies, we determined single-particle cryo-electron microscopy structures in complex with C4b at 3.4-4 Å resolution. The structures rationalize the observed functional effects of the nanobodies and define their mode of action during complement activation. Thus, we characterized seven anti-C4b nanobodies with diverse effects on the classical pathway of complement activation that may be explored for imaging, diagnostic, or therapeutic applications.
History
DepositionNov 27, 2020-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMay 4, 2022-
Current statusMay 4, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b2q
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b2q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11990.png

Downloads & links

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Map

FileDownload / File: emd_11990.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer-postprocessed, local-sharpened cryo-EM density map of complement C4b in complex with nanobody B12.
Voxel sizeX=Y=Z: 1.0285 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.0017548444 - 2.131828
Average (Standard dev.)0.0009747615 (±0.0221062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 308.55 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.02851.02851.0285
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z308.550308.550308.550
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0022.1320.001

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Supplemental data

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Mask #1

Fileemd_11990_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local-resolution filtered, sharpened cryo-EM density map of complement...

Fileemd_11990_additional_1.map
AnnotationLocal-resolution filtered, sharpened cryo-EM density map of complement C4b in complex with nanobody B12. Used for model refinements.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refined, unsharpened cryo-EM density map of complement C4b...

Fileemd_11990_additional_2.map
AnnotationRefined, unsharpened cryo-EM density map of complement C4b in complex with nanobody B12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the refinement of the...

Fileemd_11990_half_map_1.map
AnnotationHalf map 2 of the refinement of the cryo-EM density map of complement C4b in complex with nanobody B12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the refinement of the...

Fileemd_11990_half_map_2.map
AnnotationHalf map 1 of the refinement of the cryo-EM density map of complement C4b in complex with nanobody B12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complement C4b bound to nanobody B12

EntireName: Complement C4b bound to nanobody B12
Components
  • Complex: Complement C4b bound to nanobody B12
    • Complex: Complement C4 beta chain
      • Protein or peptide: Complement C4 beta chain
    • Complex: Complement C4 alpha chain
      • Protein or peptide: Complement C4 alpha chain
    • Complex: Complement C4 gamma chain
      • Protein or peptide: Complement C4 gamma chain
    • Complex: Nanobody B12
      • Protein or peptide: Anti-C4b nanobody B12
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complement C4b bound to nanobody B12

SupramoleculeName: Complement C4b bound to nanobody B12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: The purchased C4b is generated from a mixture of C4A and C4B. C4b is modelled with the sequence of C4A based on pdb 5jtw.
Molecular weightTheoretical: 204 KDa

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Supramolecule #2: Complement C4 beta chain

SupramoleculeName: Complement C4 beta chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72 KDa

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Supramolecule #3: Complement C4 alpha chain

SupramoleculeName: Complement C4 alpha chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84 KDa

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Supramolecule #4: Complement C4 gamma chain

SupramoleculeName: Complement C4 gamma chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33 KDa

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Supramolecule #5: Nanobody B12

SupramoleculeName: Nanobody B12 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21 Codon Plus (DE3)-RIL / Recombinant plasmid: pHEN6-Thrombin-his
Molecular weightTheoretical: 15 KDa

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Macromolecule #1: Complement C4 beta chain

MacromoleculeName: Complement C4 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 71.761688 KDa
SequenceString: KPRLLLFSPS VVHLGVPLSV GVQLQDVPRG QVVKGSVFLR NPSRNNVPCS PKVDFTLSSE RDFALLSLQV PLKDAKSCGL HQLLRGPEV QLVAHSPWLK DSLSRTTNIQ GINLLFSSRR GHLFLQTDQP IYNPGQRVRY RVFALDQKMR PSTDTITVMV E NSHGLRVR ...String:
KPRLLLFSPS VVHLGVPLSV GVQLQDVPRG QVVKGSVFLR NPSRNNVPCS PKVDFTLSSE RDFALLSLQV PLKDAKSCGL HQLLRGPEV QLVAHSPWLK DSLSRTTNIQ GINLLFSSRR GHLFLQTDQP IYNPGQRVRY RVFALDQKMR PSTDTITVMV E NSHGLRVR KKEVYMPSSI FQDDFVIPDI SEPGTWKISA RFSDGLESNS STQFEVKKYV LPNFEVKITP GKPYILTVPG HL DEMQLDI QARYIYGKPV QGVAYVRFGL LDEDGKKTFF RGLESQTKLV NGQSHISLSK AEFQDALEKL NMGITDLQGL RLY VAAAII ESPGGEMEEA ELTSWYFVSS PFSLDLSKTK RHLVPGAPFL LQALVREMSG SPASGIPVKV SATVSSPGSV PEVQ DIQQN TDGSGQVSIP IIIPQTISEL QLSVSAGSPH PAIARLTVAA PPSGGPGFLS IERPDSRPPR VGDTLNLNLR AVGSG ATFS HYYYMILSRG QIVFMNREPK RTLTSVSVFV DHHLAPSFYF VAFYYHGDHP VANSLRVDVQ AGACEGKLEL SVDGAK QYR NGESVKLHLE TDSLALVALG ALDTALYAAG SKSHKPLNMG KVFEAMNSYD LGCGPGGGDS ALQVFQAAGL AFSDGDQ WT LSRKRLSCPK EKTT

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Macromolecule #2: Complement C4 alpha chain

MacromoleculeName: Complement C4 alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 84.270055 KDa
SequenceString: NVNFQKAINE KLGQYASPTA KRCCQDGVTR LPMMRSCEQR AARVQQPDCR EPFLSCCQFA ESLRKKSRDK GQAGLQRALE ILQEEDLID EDDIPVRSFF PENWLWRVET VDRFQILTLW LPDSLTTWEI HGLSLSKTKG LCVATPVQLR VFREFHLHLR L PMSVRRFE ...String:
NVNFQKAINE KLGQYASPTA KRCCQDGVTR LPMMRSCEQR AARVQQPDCR EPFLSCCQFA ESLRKKSRDK GQAGLQRALE ILQEEDLID EDDIPVRSFF PENWLWRVET VDRFQILTLW LPDSLTTWEI HGLSLSKTKG LCVATPVQLR VFREFHLHLR L PMSVRRFE QLELRPVLYN YLDKNLTVSV HVSPVEGLCL AGGGGLAQQV LVPAGSARPV AFSVVPTAAA AVSLKVVARG SF EFPVGDA VSKVLQIEKE GAIHREELVY ELNPLDHRGR TLEIPGNSDP NMIPDGDFNS YVRVTASDPL DTLGSEGALS PGG VASLLR LPRGCGEQTM IYLAPTLAAS RYLDKTEQWS TLPPETKDHA VDLIQKGYMR IQQFRKADGS YAAWLSRDSS TWLT AFVLK VLSLAQEQVG GSPEKLQETS NWLLSQQQAD GSFQDPCPVL DRSMQGGLVG NDETVALTAF VTIALHHGLA VFQDE GAEP LKQRVEASIS KANSFLGEKA SAGLLGAHAA AITAYALSLT KAPVDLLGVA HNNLMAMAQE TGDNLYWGSV TGSQSN AVS PTPAPRNPSD PMPQAPALWI ETTAYALLHL LLHEGKAEMA DQASAWLTRQ GSFQGGFRST QDTVIALDAL SAYWIAS HT TEERGLNVTL SSTGRNGFKS HALQLNNRQI RGLEEELQFS LGSKINVKVG GNSKGTLKVL RTYNVLDMKN TTCQDLQI E VTVKGHVEYT MEANEDYEDY EYDELPAKDD PDAPLQPVTP LQLFEG

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Macromolecule #3: Complement C4 gamma chain

MacromoleculeName: Complement C4 gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 33.115629 KDa
SequenceString: EAPKVVEEQE SRVHYTVCIW RNGKVGLSGM AIADVTLLSG FHALRADLEK LTSLSDRYVS HFETEGPHVL LYFDSVPTSR ECVGFEAVQ EVPVGLVQPA SATLYDYYNP ERRCSVFYGA PSKSRLLATL CSAEVCQCAE GKCPRQRRAL ERGLQDEDGY R MKFACYYP ...String:
EAPKVVEEQE SRVHYTVCIW RNGKVGLSGM AIADVTLLSG FHALRADLEK LTSLSDRYVS HFETEGPHVL LYFDSVPTSR ECVGFEAVQ EVPVGLVQPA SATLYDYYNP ERRCSVFYGA PSKSRLLATL CSAEVCQCAE GKCPRQRRAL ERGLQDEDGY R MKFACYYP RVEYGFQVKV LREDSRAAFR LFETKITQVL HFTKDVKAAA NQMRNFLVRA SCRLRLEPGK EYLIMGLDGA TY DLEGHPQ YLLDSNSWIE EMPSERLCRS TRQRAACAQL NDFLQEYGTQ GCQV

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Macromolecule #4: Anti-C4b nanobody B12

MacromoleculeName: Anti-C4b nanobody B12 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.272975 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
EVQLVESGGG LVQAGGSLRL SCVASERTYM AWFRQAPGKE REFVAAITSS GMMTEYAPSV KGRFTISRDN AKNTVYLQMN SLKPEDTAV YYCAADLRQR FGERVTEYDY WGQGTQVTVS SHGSGLVPRG SGGGHHHHHH

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
10.0 mMNaPO4sodium phosphate
145.0 mMNaClSodium chloridesodium chloride

Details: 1x PBS.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot 4.5 seconds, force 1.
DetailsPurified components were mixed before vitrification.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 1453 / Average exposure time: 6.4 sec. / Average electron dose: 53.9 e/Å2 / Details: 32 frames of 0.2 seconds.
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 602481
CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4xam
PDB Unreleased entry


Details: First crystal structure of C4b.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Performed in RELION
Final 3D classificationNumber classes: 5 / Avg.num./class: 113779 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Performed in RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 128161
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5jtw

chain_id: A

5jtw

chain_id: B

5jtw

chain_id: C
DetailsModel was refined in the local-resolution filtered Relion map using Phenix real space refine.
RefinementSpace: REAL / Target criteria: Map to model FSC
Output model

PDB-7b2q:
Cryo-EM structure of complement C4b in complex with nanobody B12

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