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- EMDB-52659: A subunit of alpha-1 antitrypsin polymers isolated from ZZ explan... -

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Basic information

Entry
Database: EMDB / ID: EMD-52659
TitleA subunit of alpha-1 antitrypsin polymers isolated from ZZ explant liver tissue and decorated with conformationally nonselective Fab 9C5
Map dataThe EM map of the monomer of ex vivo ZZ alpha-1 antitrypsin polymers in complex with a conformationally unselective Fab fragment.
Sample
  • Complex: Complex of the 9C5 Fab fragment and a subunit of polymers of the severe deficiency Z alpha-1 antitrypsin variant
    • Complex: Alpha-1 antitrypsin Z variant
      • Protein or peptide: Alpha-1 antitrypsin Z variant
    • Complex: 9C5 Fab
      • Protein or peptide: 9C5 Fab heavy chain
      • Protein or peptide: 9C5 Fab light chain
KeywordsAlpha-1 antitrypsin / Alpha-1 antitrypsin polymer / Antitrypsin / AAT / Serpin / Serine protease inhibitor / Misfolding / Protein misfolding / Protein oligomer / Oligomerisation / Cirrhosis / Liver tissue / Ex-vivo polymer / Antibody / Antibody-antigen complex / Complex / Fragment antigen-binding region / Fab / PROTEIN BINDING
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / : / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsAldobiyan IF / Irving JA / Orlova EV / Lomas DA
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other privateAlpha-1 Foundation to JAI 1036784
Other governmentNIHR Investigator awarded to DAL
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The mechanism of pathogenic α-antitrypsin aggregation in the human liver.
Authors: Ibrahim Aldobiyan / Emma L K Elliston / Narinder Heyer-Chauhan / Stefan T Arold / Lingyun Zhao / Brandon Huntington / Sarah M Lowen / Elena V Orlova / James A Irving / David A Lomas /
Abstract: Originating 2 to 3 millennia ago in a Scandinavian population, the SERPINA1 Z allele (Glu342Lys) is present in up to 2.5% of populations of Northern European descent and accounts for 95% of severe α- ...Originating 2 to 3 millennia ago in a Scandinavian population, the SERPINA1 Z allele (Glu342Lys) is present in up to 2.5% of populations of Northern European descent and accounts for 95% of severe α-antitrypsin deficiency. The α-antitrypsin Z variant self-assembles into polymer chains that deposit within hepatocytes, predisposing to liver disease. Here, the 4.0Å subunit structure of polymers isolated directly from human liver tissue has been determined using cryoelectron microscopy. Challenges of flexibility, small subunit size, heterogeneous length, and preferred orientations were mitigated using antibody Fab domains and sample preparation strategies. This structure demonstrates that the formation of polymers in vivo involves self-incorporation of an exposed structural element (the reactive center loop) as an additional β-strand into the central β-sheet of α-antitrypsin and displacement of a C-terminal region from one subunit with incorporation into the next. Unlike amyloid aggregation, this well-folded structure partially recapitulates a conformation adopted during normal function of the protein. These perturbations to the constituent α-antitrypsin subunits of human tissue-derived polymers are consistent with a pronounced stability, their tendency toward long-chain forms, the ability of a subset to undergo canonical secretion, and the action of a class of small molecules that block polymerization in vivo.
History
DepositionJan 31, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52659.png

Downloads & links

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Map

FileDownload / File: emd_52659.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of the monomer of ex vivo ZZ alpha-1 antitrypsin polymers in complex with a conformationally unselective Fab fragment.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 180 pix.
= 167.4 Å		0.93 Å/pix.
x 180 pix.
= 167.4 Å		0.93 Å/pix.
x 180 pix.
= 167.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00516
Minimum - Maximum-0.00717385 - 0.020572502
Average (Standard dev.)0.00012656288 (±0.0010935802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 167.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52659_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The post-processed EM map (masked). B-factor 150.

Fileemd_52659_additional_1.map
AnnotationThe post-processed EM map (masked). B-factor 150.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The post-processed EM map. B-factor 150.

Fileemd_52659_additional_2.map
AnnotationThe post-processed EM map. B-factor 150.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of: The EM map of the...

Fileemd_52659_half_map_1.map
AnnotationHalf-map 1 of: The EM map of the monomer of ex vivo ZZ alpha-1 antitrypsin polymers in complex with a conformationally unselective Fab fragment.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of: The EM map of the...

Fileemd_52659_half_map_2.map
AnnotationHalf-map 2 of: The EM map of the monomer of ex vivo ZZ alpha-1 antitrypsin polymers in complex with a conformationally unselective Fab fragment.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the 9C5 Fab fragment and a subunit of polymers of the ...

EntireName: Complex of the 9C5 Fab fragment and a subunit of polymers of the severe deficiency Z alpha-1 antitrypsin variant
Components
  • Complex: Complex of the 9C5 Fab fragment and a subunit of polymers of the severe deficiency Z alpha-1 antitrypsin variant
    • Complex: Alpha-1 antitrypsin Z variant
      • Protein or peptide: Alpha-1 antitrypsin Z variant
    • Complex: 9C5 Fab
      • Protein or peptide: 9C5 Fab heavy chain
      • Protein or peptide: 9C5 Fab light chain

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Supramolecule #1: Complex of the 9C5 Fab fragment and a subunit of polymers of the ...

SupramoleculeName: Complex of the 9C5 Fab fragment and a subunit of polymers of the severe deficiency Z alpha-1 antitrypsin variant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: Alpha-1 antitrypsin Z variant

SupramoleculeName: Alpha-1 antitrypsin Z variant / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: The Z severe deficiency variant of alpha-1 antitrypsin.
Source (natural)Organism: Homo sapiens (human) / Organ: Liver / Tissue: Explant liver tissue / Organelle: ER-derived / Location in cell: Inclusion bodies

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Supramolecule #3: 9C5 Fab

SupramoleculeName: 9C5 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse) / Strain: BALB/c / Organ: Spleen / Location in cell: Secreted

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Macromolecule #1: Alpha-1 antitrypsin Z variant

MacromoleculeName: Alpha-1 antitrypsin Z variant / type: protein_or_peptide / ID: 1
Details: The Z severe deficiency variant of alpha-1 antitrypsin E342K variant
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Liver / Tissue: Explant tissue
SequenceString: MPSSVSWGIL LLAGLCCLVP VSLAEDPQGD AAQKTDTSHH DQDHPTFNKI TPNLAEFAFS LYRQLAHQSN STNIFFSPVS IATAFAMLSL GTKADTHDEI LEGLNFNLTE IPEAQIHEGF QELLRTLNQP DSQLQLTTGN GLFLSEGLKL VDKFLEDVKK LYHSEAFTVN ...String:
MPSSVSWGIL LLAGLCCLVP VSLAEDPQGD AAQKTDTSHH DQDHPTFNKI TPNLAEFAFS LYRQLAHQSN STNIFFSPVS IATAFAMLSL GTKADTHDEI LEGLNFNLTE IPEAQIHEGF QELLRTLNQP DSQLQLTTGN GLFLSEGLKL VDKFLEDVKK LYHSEAFTVN FGDTEEAKKQ INDYVEKGTQ GKIVDLVKEL DRDTVFALVN YIFFKGKWER PFEVKDTEEE DFHVDQVTTV KVPMMKRLGM FNIQHCKKLS SWVLLMKYLG NATAIFFLPD EGKLQHLENE LTHDIITKFL ENEDRRSASL HLPKLSITGT YDLKSVLGQL GITKVFSNGA DLSGVTEEAP LKLSKAVHKA VLTIDKKGTE AAGAMFLEAI PMSIPPEVKF NKPFVFLMIE QNTKSPLFMG KVVNPTQK

UniProtKB: Alpha-1-antitrypsin

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Macromolecule #2: 9C5 Fab heavy chain

MacromoleculeName: 9C5 Fab heavy chain / type: protein_or_peptide / ID: 2
Details: Heavy chain of the Fab fragment of a conformationally nonselective antibody (9C5) that binds to alpha-1-antitrypsin
Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: BALB/c / Organ: Spleen
SequenceString: QVQLQQSGAE LVKPGASVKL SCTATGFNIK DTYMHWVKQR PEQGLEWIGR IDPANGNTKY DPKFQGKATL TADTSSNTAY LQLSSLTSED TAVYYCARKR YSMDYWGQGT SVTVSSAKTT PPSVYPLAPG SGAQTNSMVT LGCLVKGYFP EPVTVTWNSG SLSSGVHTFP ...String:
QVQLQQSGAE LVKPGASVKL SCTATGFNIK DTYMHWVKQR PEQGLEWIGR IDPANGNTKY DPKFQGKATL TADTSSNTAY LQLSSLTSED TAVYYCARKR YSMDYWGQGT SVTVSSAKTT PPSVYPLAPG SGAQTNSMVT LGCLVKGYFP EPVTVTWNSG SLSSGVHTFP AVLQSDLYTL SSSVTVPSST WPSETVTCNV AHPASSTKVD KKIVPRD

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Macromolecule #3: 9C5 Fab light chain

MacromoleculeName: 9C5 Fab light chain / type: protein_or_peptide / ID: 3
Details: Light chain of the Fab fragment of a conformationally nonselective antibody (9C5) that binds to alpha-1-antitrypsin
Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: BALB/c / Organ: Spleen
SequenceString: SIVMTQTPKF LLVSAGERVT ITCKASQSVS NDVGWYQQKP GQPPKLLIYN ASNRKNGVPD RFTGSGYGTD FTFTISTVQA EDLAVYFCQQ DHSFPLKFGA GTKLELKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD ...String:
SIVMTQTPKF LLVSAGERVT ITCKASQSVS NDVGWYQQKP GQPPKLLIYN ASNRKNGVPD RFTGSGYGTD FTFTISTVQA EDLAVYFCQQ DHSFPLKFGA GTKLELKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RNE

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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 #1

Preparation ID1
Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris
50.0 mMNaClSodium chloride
5.0 MmEDTA

Details: 50mM Tris pH 7.4, 50mM NaCl, 5mM EDTA, 0.02 % (w/v) NaN3
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Incubation time: 0s Blot time: 3.5s Blot force: 0s.
DetailsThe sample comprised a mixed population of unbranched Z alpha-1 antirypsin polymers of varying length (primarily between 4-6 subunits), labelled with the Fab fragment of the 9C5 antibody

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Sample preparation #2

Preparation ID2
Concentration0.05 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris
50.0 mMNaClSodium chloride
5.0 MmEDTA

Details: 50mM Tris pH 7.4, 50mM NaCl, 5mM EDTA, 0.02 % (w/v) NaN3
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Incubation time: 0s Blot time: 3.5s Blot force: 0s.
DetailsThe sample comprised a mixed population of unbranched Z alpha-1 antirypsin polymers of varying length (primarily between 4-6 subunits), labelled with the Fab fragment of the 9C5 antibody

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Sample preparation #3

Preparation ID3
Concentration0.05 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris
50.0 mMNaClSodium chloride
5.0 MmEDTA

Details: 50mM Tris pH 7.4, 50mM NaCl, 5mM EDTA, 0.02 % (w/v) NaN3
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Incubation time: 0s Blot time: 3.5s Blot force: 0s.
DetailsThe sample comprised a mixed population of unbranched Z alpha-1 antirypsin polymers of varying length (primarily between 4-6 subunits), labelled with the Fab fragment of the 9C5 antibody

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
TemperatureMin: 88.0 K / Max: 89.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 1 / Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 11968 / Average exposure time: 4.0 sec. / Average electron dose: 49.81 e/Å2
Details: Each movie had 1323 raw frames 2 shots per hole Data was collected on a TFS Krios G4 fitted with a (Selectrix X energy filter using a slit width of 20 eV)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 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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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
TemperatureMin: 88.0 K / Max: 89.0 K
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 15366 / Average exposure time: 1.15 sec. / Average electron dose: 43.55 e/Å2
Details: Hardware microscope Titan Krios D3771 acceleration voltage keV 300 detector post GIF K3 detector mode super resolution bin 2 Data acquisition parameters nominal magnification 130kx pixel ...Details: Hardware microscope Titan Krios D3771 acceleration voltage keV 300 detector post GIF K3 detector mode super resolution bin 2 Data acquisition parameters nominal magnification 130kx pixel size A 0.65 spot size 4 illuminated area um 0.88 Dose dose per pixel per second e: 18.4 e/px/s dose per A2 per second e: 43.55 e/A2 exposure time s 1.15 number of fractions 50 if Falcon used were the frames aligned no Data collection parameters defocus range from -2.7 defocus range to -1.5 autofocus after centering drift measurement none delay after stage shift s 4. delay after image shift s 0.75 exposures per hole 3 Apertures, size in um c1 2000 c2 50 c3 2000 objective 100 number of images ~15,000 at 3 shots per hole, faster data acquisition, ~640 images per hr Gatan energy filter with a 20 eV slit was used during data collection
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
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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Electron microscopy #1~~

Microscopy ID1
MicroscopeTFS KRIOS
TemperatureMin: 88.0 K / Max: 89.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 3 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7982 / Average exposure time: 1.05 sec. / Average electron dose: 38.32 e/Å2
Details: Hardware microscope Titan Krios D3771 acceleration voltage keV 300 detector post GIF K3 detector mode super resolution bin 2 Data acquisition parameters nominal magnification 130kx pixel ...Details: Hardware microscope Titan Krios D3771 acceleration voltage keV 300 detector post GIF K3 detector mode super resolution bin 2 Data acquisition parameters nominal magnification 130kx pixel size A 0.65 spot size 4 illuminated area um 0.92 Dose dose per pixel per second e: 16.2 e/px/s dose per A2 per second e: 38.32 e/A2 exposure time s 1.05 number of fractions 40 if Falcon used were the frames aligned no Data collection parameters defocus range from -2.7 defocus range to -1.5 autofocus after centering drift measurement none delay after stage shift s 4. delay after image shift s 0.75 exposures per hole 3 Apertures, size in um c1 2000 c2 70 c3 2000 objective 100 number of images ~8,000 at 2 shots per hole, faster data acquisition, ~730 images per hr Gatan energy filter with a 20 eV slit was used during data collection
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.7 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

Image recording ID1
Particle selectionNumber selected: 5084114
CTF correctionSoftware: (Name: CTFFIND (ver. 4.0), CTFFIND (ver. 4.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The initial reference was a lower-resolution cryo-EM map of the Z alpha-1 antitrypsin polymer sample decorated with an alternative Fab fragment (4B12) which had been refined to a nominal 5. ...Details: The initial reference was a lower-resolution cryo-EM map of the Z alpha-1 antitrypsin polymer sample decorated with an alternative Fab fragment (4B12) which had been refined to a nominal 5.7A resolution. The density of antitrypsin remained the same, and the density for the fab fragment was reoriented to correspond with the known epitope of the 9C5 fab - The crystal structure of the complex between antytrpsin and 9C5 Fab has been deposited into the PDB (Accession code 9HUD). During the first round of 3D classification the model was low-pass filtered to 20A. The map was binarise and a large soft-edged mask was used (binary map was extended by 7 pixels, soft-edge of 11 pixels)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta-2) / Number images used: 273961
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta-2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 354230 / Software - Name: RELION (ver. 5.0) / Details: Class 1: 273961 Class 2: 307137 Class 3: 481591
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

9hud

chain_id: A, residue_range: 1-354, source_name: PDB, initial_model_type: experimental modelAlpha-1 antitrypsin N-terminal fragment

9hud

chain_id: B, residue_range: 362-393, source_name: PDB, initial_model_type: experimental modelAlpha-1 antitrypsin C-terminal fragment

9hud

chain_id: H, residue_range: 1-213, source_name: PDB, initial_model_type: experimental model9C5 Fab heavy chain

9hud

chain_id: L, residue_range: 1-213, source_name: PDB, initial_model_type: experimental model9C5 Fab light chain
DetailsRigid body fitting into the EM density was performed in ChimeraX using the backbone trace of the crystal structure of the complex between the RCL-inserted form of alpha-1-antitrypsin and 9C5 Fab
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient

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