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- EMDB-75834: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compsta... -

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Entry
Database: EMDB / ID: EMD-75834
TitleCryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1
Map dataNon-uniform refinement EMReady Map Sharpening C3bB-Cp60 TED Conformation 1
Sample
  • Complex: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1
    • Protein or peptide: Complement C3 beta chain
    • Protein or peptide: Compstatin Cp60
    • Protein or peptide: Complement C3b alpha' chain
    • Protein or peptide: Complement factor B
  • Ligand: NICKEL (II) ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplement System / C3 / Alternate Pathway / C3 Pro-Convertase / C3b / Factor B / Compstatin / IMMUNE SYSTEM
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / complement binding / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning ...alternative-complement-pathway C3/C5 convertase / complement binding / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 / positive regulation of lipid storage / complement activation, GZMK pathway / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / symbiont cell surface / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement receptor mediated signaling pathway / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / complement activation, classical pathway / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / positive regulation of protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / endoplasmic reticulum lumen / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / signaling receptor binding / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement factor B / Complement B/C2 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site ...Complement factor B / Complement B/C2 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Immunoglobulin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Complement factor B / Complement C3
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsHerbine K / Lambris J
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
Citation
Journal: J Med Chem / Year: 2026
Title: New Analogs of the Compstatin Family of Clinical Complement Inhibitors with Low Picomolar Target Affinity.
Authors: Stephanie A Vogt / Alexander J Lander / Karl Herbine / Ekaterina Umnyakova / Jannes Felsch / Roman Aschwanden / Sarah E Hughes / Oliver Schwardt / Markus A Lill / Martin Smieško / John D ...Authors: Stephanie A Vogt / Alexander J Lander / Karl Herbine / Ekaterina Umnyakova / Jannes Felsch / Roman Aschwanden / Sarah E Hughes / Oliver Schwardt / Markus A Lill / Martin Smieško / John D Lambris / Christina Lamers / Daniel Ricklin /
Abstract: Compstatin-class macrocyclic peptides have emerged as therapeutic complement modulators, with a PEGylated compstatin derivative being approved and sequence-optimized analogs with enhanced PK/PD ...Compstatin-class macrocyclic peptides have emerged as therapeutic complement modulators, with a PEGylated compstatin derivative being approved and sequence-optimized analogs with enhanced PK/PD properties showing clinical promise. By extending structure-activity relationship studies of compstatin, we identified a modification (V3I) that enhances the target affinity up to 30-fold. Analog Cp01-V3I represents the most potent proteinogenic compstatin ( = 20 nM), opening paths toward recombinant applications. Introducing the V3I modification into late-generation compstatin analogs yielded a low-picomolar-affinity derivative ( = 0.08 nM), termed Cp60, featuring potent complement inhibition in vitro. Cryogenic electron microscopy of the C3bB-Cp60 complex at 2.88 Å resolution confirmed the structural basis for enhanced target affinity and provided mechanistic insights. Lastly, we demonstrate that Cp60s ultralong target residence time enables diagnostic applications for detecting complement opsonins on biosurfaces. Collectively, this work highlights the importance of rigorous optimization of de novo peptide inhibitors to improve PK/PD properties and enable novel applications.
#1: Journal: To Be Published
Title: New analogs of the compstatin family of clinical complement inhibi-tors with low picomolar target affinity
Authors: Herbine K / Lambris J
History
DepositionMar 4, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_75834.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-uniform refinement EMReady Map Sharpening C3bB-Cp60 TED Conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 358.771 Å
0.93 Å/pix.
x 384 pix.
= 358.771 Å
0.93 Å/pix.
x 384 pix.
= 358.771 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9343 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.14215761 - 21.322454
Average (Standard dev.)-0.01905756 (±0.46644428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 358.7712 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Non-uniform refinement C3bB-Cp60 TED Conformation 1

Fileemd_75834_additional_1.map
AnnotationNon-uniform refinement C3bB-Cp60 TED Conformation 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Non-uniform refinement (Half Map 1) C3bB-Cp60 TED Conformation 1

Fileemd_75834_half_map_1.map
AnnotationNon-uniform refinement (Half Map 1) C3bB-Cp60 TED Conformation 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Non-uniform refinement (Half Map 2) C3bB-Cp60 TED Conformation 1

Fileemd_75834_half_map_2.map
AnnotationNon-uniform refinement (Half Map 2) C3bB-Cp60 TED Conformation 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compsta...

EntireName: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1
Components
  • Complex: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1
    • Protein or peptide: Complement C3 beta chain
    • Protein or peptide: Compstatin Cp60
    • Protein or peptide: Complement C3b alpha' chain
    • Protein or peptide: Complement factor B
  • Ligand: NICKEL (II) ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compsta...

SupramoleculeName: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 256 KDa

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Macromolecule #1: Complement C3 beta chain

MacromoleculeName: Complement C3 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.39332 KDa
SequenceString: SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQAT FGTQVVEKVV LVSLQSGYLF IQTDKTIYTP GSTVLYRIFT VNHKLLPVGR TVMVNIENPE GIPVKQDSLS S QNQLGVLP ...String:
SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQAT FGTQVVEKVV LVSLQSGYLF IQTDKTIYTP GSTVLYRIFT VNHKLLPVGR TVMVNIENPE GIPVKQDSLS S QNQLGVLP LSWDIPELVN MGQWKIRAYY ENSPQQVFST EFEVKEYVLP SFEVIVEPTE KFYYIYNEKG LEVTITARFL YG KKVEGTA FVIFGIQDGE QRISLPESLK RIPIEDGSGE VVLSRKVLLD GVQNPRAEDL VGKSLYVSAT VILHSGSDMV QAE RSGIPI VTSPYQIHFT KTPKYFKPGM PFDLMVFVTN PDGSPAYRVP VAVQGEDTVQ SLTQGDGVAK LSINTHPSQK PLSI TVRTK KQELSEAEQA TRTMQALPYS TVGNSNNYLH LSVLRTELRP GETLNVNFLL RMDRAHEAKI RYYTYLIMNK GRLLK AGRQ VREPGQDLVV LPLSITTDFI PSFRLVAYYT LIGASGQREV VADSVWVDVK DSCVGSLVVK SGQSEDRQPV PGQQMT LKI EGDHGARVVL VAVDKGVFVL NKKNKLTQSK IWDVVEKADI GCTPGSGKDY AGVFSDAGLT FTSSSGQQTA QRAELQC PQ PAA

UniProtKB: Complement C3

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Macromolecule #2: Complement C3b alpha' chain

MacromoleculeName: Complement C3b alpha' chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.073164 KDa
SequenceString: SNLDEDIIAE ENIVSRSEFP ESWLWNVEDL KEPPKNGIST KLMNIFLKDS ITTWEILAVS MSDKKGICVA DPFEVTVMQD FFIDLRLPY SVVRNEQVEI RAVLYNYRQN QELKVRVELL HNPAFCSLAT TKRRHQQTVT IPPKSSLSVP YVIVPLKTGL Q EVEVKAAV ...String:
SNLDEDIIAE ENIVSRSEFP ESWLWNVEDL KEPPKNGIST KLMNIFLKDS ITTWEILAVS MSDKKGICVA DPFEVTVMQD FFIDLRLPY SVVRNEQVEI RAVLYNYRQN QELKVRVELL HNPAFCSLAT TKRRHQQTVT IPPKSSLSVP YVIVPLKTGL Q EVEVKAAV YHHFISDGVR KSLKVVPEGI RMNKTVAVRT LDPERLGREG VQKEDIPPAD LSDQVPDTES ETRILLQGTP VA QMTEDAV DAERLKHLIV TPSGCGEQNM IGMTPTVIAV HYLDETEQWE KFGLEKRQGA LELIKKGYTQ QLAFRQPSSA FAA FVKRAP STWLTAYVVK VFSLAVNLIA IDSQVLCGAV KWLILEKQKP DGVFQEDAPV IHQEMIGGLR NNNEKDMALT AFVL ISLQE AKDICEEQVN SLPGSITKAG DFLEANYMNL QRSYTVAIAG YALAQMGRLK GPLLNKFLTT AKDKNRWEDP GKQLY NVEA TSYALLALLQ LKDFDFVPPV VRWLNEQRYY GGGYGSTQAT FMVFQALAQY QKDAPDHQEL NLDVSLQLPS RSSKIT HRI HWESASLLRS EETKENEGFT VTAEGKGQGT LSVVTMYHAK AKDQLTCNKF DLKVTIKPAP ETEKRPQDAK NTMILEI CT RYRGDQDATM SILDISMMTG FAPDTDDLKQ LANGVDRYIS KYELDKAFSD RNTLIIYLDK VSHSEDDCLA FKVHQYFN V ELIQPGAVKV YAYYNLEESC TRFYHPEKED GKLNKLCRDE LCRCAEENCF IQKSDDKVTL EERLDKACEP GVDYVYKTR LVKVQLSNDF DEYIMAIEQT IKSGSDEVQV GQQRTFISPI KCREALKLEE KKHYLMWGLS SDFWGEKPNL SYIIGKDTWV EHWPEEDEC QDEENQKQCQ DLGAFTESMV VFGCPN

UniProtKB: Complement C3

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Macromolecule #3: Compstatin Cp60

MacromoleculeName: Compstatin Cp60 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.066493 KDa
SequenceString:
(DTY)ICI(EXL)QDW(SAR)A HRC(IML)KK

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Macromolecule #4: Complement factor B

MacromoleculeName: Complement factor B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: alternative-complement-pathway C3/C5 convertase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.10975 KDa
SequenceString: TPWSLARPQG SCSLEGVEIK GGSFRLLQEG QALEYVCPSG FYPYPVQTRT CRSTGSWSTL KTQDQKTVRK AECRAIHCPR PHDFENGEY WPRSPYYNVS DEISFHCYDG YTLRGSANRT CQVNGRWSGQ TAICDNGAGY CSNPGIPIGT RKVGSQYRLE D SVTYHCSR ...String:
TPWSLARPQG SCSLEGVEIK GGSFRLLQEG QALEYVCPSG FYPYPVQTRT CRSTGSWSTL KTQDQKTVRK AECRAIHCPR PHDFENGEY WPRSPYYNVS DEISFHCYDG YTLRGSANRT CQVNGRWSGQ TAICDNGAGY CSNPGIPIGT RKVGSQYRLE D SVTYHCSR GLTLRGSQRR TCQEGGSWSG TEPSCQDSFM YDTPQEVAEA FLSSLTETIE GVDAEDGHGP GEQQKRKIVL DP SGSMNIY LVLDGSDSIG ASNFTGAKKC LVNLIEKVAS YGVKPRYGLV TYATYPKIWV KVSEADSSNA DWVTKQLNEI NYE DHKLKS GTNTKKALQA VYSMMSWPDD VPPEGWNRTR HVIILMTDGL HNMGGDPITV IDEIRDLLYI GKDRKNPRED YLDV YVFGV GPLVNQVNIN ALASKKDNEQ HVFKVKDMEN LEDVFYQMID ESQSLSLCGM VWEHRKGTDY HKQPWQAKIS VIRPS KGHE SCMGAVVSEY FVLTAAHCFT VDDKEHSIKV SVGGEKRDLE IEVVLFHPNY NINGKKEAGI PEFYDYDVAL IKLKNK LKY GQTIRPICLP CTEGTTRALR LPPTTTCQQQ KEELLPAQDI KALFVSEEEK KLTRKEVYIK NGDKKGSCER DAQYAPG YD KVKDISEVVT PRFLCTGGVS PYADPNTCRG DSGGPLIVHK RSRFIQVGVI SWGVVDVCKN QKRQKQVPAH ARDFHINL F QVLPWLKEKL QDEDLGFL

UniProtKB: Complement factor B

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Macromolecule #6: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.67 mg/mL
BufferpH: 7.5
Details: 20 mM Tris-HCl pH 7.5, 140 mM NaCl, and 10 mM NiCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Negatively glow-discharged with 15 mA for 60 seconds using a PELCO easiGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details3 uM C3b and FB were mixed with Cp60 at 1:1:2 molar ratio in buffer containing 20 mM Tris-HCl pH 7.5, 140 mM NaCl, and 10 mM NiCl2, and incubated on ice for 1 hour prior to vitrification.

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
SoftwareName: EPU (ver. 3.14)
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 6993 / Average exposure time: 6.0 sec. / Average electron dose: 43.36 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1475831
Details: Automated particle picking (Blob and Template picker, CryoSPARC) with manual inspection and micrograph junk detector
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 143730
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.9.8.96)
DetailsInitial docking of starting model performed in ChimeraX. Flexible/Refinement performed with Phenix Real-Space Refinement. Coot used for manual fitting and inspection.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-11mg:
Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 1

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