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- EMDB-20100: B41 SOSIP.664 in complex with the silent-face antibody SF12 and V... -

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Entry
Database: EMDB / ID: EMD-20100
TitleB41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074
Map dataFinal refined sharpened map used for model building and coordinate refinement
Sample
  • Complex: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab
    • Complex: B41 SOSIP.664 trimer
      • Protein or peptide: Envelope glycoprotein gp41
      • Protein or peptide: Envelope glycoprotein gp120
    • Complex: 10-1074 Fab
      • Protein or peptide: 10-1074 Heavy Chain,10-1074 Heavy Chain
      • Protein or peptide: 10-1074 Light Chain,10-1074 Light Chain
    • Complex: SF12 Fab
      • Protein or peptide: SF12 Heavy Chain,SF12 Heavy Chain
      • Protein or peptide: SF12 Light Chain,SF12 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 broadly-neutralizing antibody / Env trimer structure / silent face / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / Immunoglobulin kappa constant / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBarnes CO / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 GM082545-06 United States
CitationJournal: Immunity / Year: 2019
Title: Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.
Authors: Till Schoofs / Christopher O Barnes / Nina Suh-Toma / Jovana Golijanin / Philipp Schommers / Henning Gruell / Anthony P West / Franziska Bach / Yu Erica Lee / Lilian Nogueira / Ivelin S ...Authors: Till Schoofs / Christopher O Barnes / Nina Suh-Toma / Jovana Golijanin / Philipp Schommers / Henning Gruell / Anthony P West / Franziska Bach / Yu Erica Lee / Lilian Nogueira / Ivelin S Georgiev / Robert T Bailer / Julie Czartoski / John R Mascola / Michael S Seaman / M Juliana McElrath / Nicole A Doria-Rose / Florian Klein / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization ...Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env's silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448 glycan. Effective bNAbs can therefore be raised against HIV-1 Env's silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.
History
DepositionApr 14, 2019-
Header (metadata) releaseMay 8, 2019-
Map releaseJun 5, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.022
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  • Surface view with fitted model
  • Atomic models: PDB-6okp
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20100.png

Downloads & links

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Map

FileDownload / File: emd_20100.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal refined sharpened map used for model building and coordinate refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.07658794 - 0.14188224
Average (Standard dev.)-0.000032784465 (±0.0046433927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0770.142-0.000

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Supplemental data

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Mask #1

Fileemd_20100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Final refined unsharpened map.

Fileemd_20100_additional.map
AnnotationFinal refined unsharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_20100_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_20100_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1...

EntireName: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab
Components
  • Complex: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab
    • Complex: B41 SOSIP.664 trimer
      • Protein or peptide: Envelope glycoprotein gp41
      • Protein or peptide: Envelope glycoprotein gp120
    • Complex: 10-1074 Fab
      • Protein or peptide: 10-1074 Heavy Chain,10-1074 Heavy Chain
      • Protein or peptide: 10-1074 Light Chain,10-1074 Light Chain
    • Complex: SF12 Fab
      • Protein or peptide: SF12 Heavy Chain,SF12 Heavy Chain
      • Protein or peptide: SF12 Light Chain,SF12 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1...

SupramoleculeName: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: Fab fragment generated by recombinant expression and complexed with the B41 SOSIP.664 trimer
Molecular weightTheoretical: 540 KDa

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Supramolecule #2: B41 SOSIP.664 trimer

SupramoleculeName: B41 SOSIP.664 trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: 10-1074 Fab

SupramoleculeName: 10-1074 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: SF12 Fab

SupramoleculeName: SF12 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: B41
Molecular weightTheoretical: 17.357824 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
AVGLGAFILG FLGAAGSTMG AASMALTVQA RLLLSGIVQQ QNNLLRAPEA QQHMLQLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KIICCTNVPW NDSWSNKTIN EIWDNMTWMQ WEKEIDNYTQ HIYTLLEVSQ IQQEKNEQEL LELD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: B41 / Cell: B-Cell
Molecular weightTheoretical: 57.702469 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCNNV NTNNTNNSTN ATISDWEKME T GEMKNCSF ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCNNV NTNNTNNSTN ATISDWEKME T GEMKNCSF NVTTSIRDKI KKEYALFYKL DVVPLENKNN INNTNITNYR LINCNTSVIT QACPKVSFEP IPIHYCAPAG FA ILKCNSK TFNGSGPCTN VSTVQCTHGI RPVVSTQLLL NGSLAEEEIV IRSENITDNA KTIIVQLNEA VEINCTRPNN NTR KSIHIG PGRAFYATGD IIGNIRQAHC NISKARWNET LGQIVAKLEE QFPNKTIIFN HSSGGDPEIV THSFNCGGEF FYCN TTPLF NSTWNNTRTD DYPTGGEQNI TLQCRIKQII NMWQGVGKAM YAPPIRGQIR CSSNITGLLL TRDGGRDQNG TETFR PGGG NMRDNWRSEL YKYKVVKIEP LGIAPTACKR RV

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 10-1074 Heavy Chain,10-1074 Heavy Chain

MacromoleculeName: 10-1074 Heavy Chain,10-1074 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Cell: B-Cell
Molecular weightTheoretical: 26.490568 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKT HH HHHH

UniProtKB: IgG H chain

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Macromolecule #4: 10-1074 Light Chain,10-1074 Light Chain

MacromoleculeName: 10-1074 Light Chain,10-1074 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Cell: B-Cell
Molecular weightTheoretical: 23.18076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYVRPLSVAL GETARISCGR QALGSRAVQW YQHRPGQAPI LLIYNNQDRP SGIPERFSGT PDINFGTRAT LTISGVEAGD EADYYCHMW DSRSGFSWSF GGATRLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
SYVRPLSVAL GETARISCGR QALGSRAVQW YQHRPGQAPI LLIYNNQDRP SGIPERFSGT PDINFGTRAT LTISGVEAGD EADYYCHMW DSRSGFSWSF GGATRLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

UniProtKB: IGL@ protein

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Macromolecule #5: SF12 Heavy Chain,SF12 Heavy Chain

MacromoleculeName: SF12 Heavy Chain,SF12 Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Cell: B-Cell
Molecular weightTheoretical: 26.045205 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSV TCRVSGGSLD LYYWSWIRQP PGKGLQWIGF VYFDGSYGDY DPSLRSRVTI SADMSKNQIS LRLKSVTPA DTAVYYCARL GPGGIFDRWT GHYGDKWLDP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
QVQLQESGPG LVKPSETLSV TCRVSGGSLD LYYWSWIRQP PGKGLQWIGF VYFDGSYGDY DPSLRSRVTI SADMSKNQIS LRLKSVTPA DTAVYYCARL GPGGIFDRWT GHYGDKWLDP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCDKTHH HH H

UniProtKB: IgG H chain

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Macromolecule #6: SF12 Light Chain,SF12 Light Chain

MacromoleculeName: SF12 Light Chain,SF12 Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.236971 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIDLTQSPRT LSLSAGERAT LLCRASQSVS NVALAWYQHK PGQAPRLLLH EASTRATGIP DRFIGSGSGR DFTLTITSLE PEDFAVYYC QLSGRRLGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD ...String:
QIDLTQSPRT LSLSAGERAT LLCRASQSVS NVALAWYQHK PGQAPRLLLH EASTRATGIP DRFIGSGSGR DFTLTITSLE PEDFAVYYC QLSGRRLGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC

UniProtKB: Immunoglobulin kappa constant

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 33 / 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

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
120.0 mMsodium chlorideNaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: 0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2732 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 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: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 676161
Details: manual picking followed by template-based autopicking
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 301920
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6ch9

chain_id: G, source_name: PDB, initial_model_type: experimental model

6ch9

chain_id: B, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6okp:
B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074

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