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- EMDB-16808: Human MUC5B amino acids 26-1435 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16808
TitleHuman MUC5B amino acids 26-1435
Map data
Sample
  • Complex: MUC5B amino acids 26-1435
    • Protein or peptide: MUC5B
KeywordsMucin / Filament / D assemblies / disulfide bonds / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / extracellular matrix / Golgi lumen / intracellular membrane-bounded organelle / extracellular space ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / extracellular matrix / Golgi lumen / intracellular membrane-bounded organelle / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
WxxW domain / Mucin-2 protein WxxW repeating region / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...WxxW domain / Mucin-2 protein WxxW repeating region / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKhmelnitsky L / Javitt G / Elad N / Fass D
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation2660/20 Israel
CitationJournal: To Be Published
Title: Pulmonary Fibrosis Mutation impairs Mucin 5B Supramolecular Assembly
Authors: Khmelnitsky L / Javitt G / Reznik N / Yeshaya N / Elad N / Anikster Y / Shalva N / Barel O / Pode-Shakked B / Greenberg LJ / Segel MJ / Fass D
History
DepositionMar 8, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16808.png

Downloads & links

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Map

FileDownload / File: emd_16808.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 700 pix.
= 578.48 Å		0.83 Å/pix.
x 700 pix.
= 578.48 Å		0.83 Å/pix.
x 700 pix.
= 578.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8264 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.056
Minimum - Maximum-0.4877545 - 0.7096858
Average (Standard dev.)0.00017814223 (±0.014285275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 578.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16808_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16808_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MUC5B amino acids 26-1435

EntireName: MUC5B amino acids 26-1435
Components
  • Complex: MUC5B amino acids 26-1435
    • Protein or peptide: MUC5B

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Supramolecule #1: MUC5B amino acids 26-1435

SupramoleculeName: MUC5B amino acids 26-1435 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MUC5B

MacromoleculeName: MUC5B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QGPVEPSWEN AGHTMDGGAP TSSPTRRVSF VPPVTVFPSL SPLNPAHNGR VCSTWGDFHY KTFDGDVFRF PGLCNYVFSE HCRAAYEDFN VQLRRGLVGS RPVVTRVVIK AQGLVLEASN GSVLINGQRE ELPYSRTGLL VEQSGDYIKV SIRLVLTFLW NGEDSALLEL ...String:
QGPVEPSWEN AGHTMDGGAP TSSPTRRVSF VPPVTVFPSL SPLNPAHNGR VCSTWGDFHY KTFDGDVFRF PGLCNYVFSE HCRAAYEDFN VQLRRGLVGS RPVVTRVVIK AQGLVLEASN GSVLINGQRE ELPYSRTGLL VEQSGDYIKV SIRLVLTFLW NGEDSALLEL DPKYANQTCG LCGDFNGLPA FNEFYAHNAR LTPLQFGNLQ KLDGPTEQCP DPLPLPAGNC TDEEGICHRT LLGPAFAECH ALVDSTAYLA ACAQDLCRCP TCPCATFVEY SRQCAHAGGQ PRNWRCPELC PRTCPLNMQH QECGSPCTDT CSNPQRAQLC EDHCVDGCFC PPGTVLDDIT HSGCLPLGQC PCTHGGRTYS PGTSFNTTCS SCTCSGGLWQ CQDLPCPGTC SVQGGAHIST YDEKLYDLHG DCSYVLSKKC ADSSFTVLAE LRKCGLTDNE NCLKAVTLSL DGGDTAIRVQ ADGGVFLNSI YTQLPLSAAN ITLFTPSSFF IVVQTGLGLQ LLVQLVPLMQ VFVRLDPAHQ GQMCGLCGNF NQNQADDFTA LSGVVEATGA AFANTWKAQA ACANARNSFE DPCSLSVENE NYARHWCSRL TDPNSAFSRC HSIINPKPFH SNCMFDTCNC ERSEDCLCAA LSSYVHACAA KGVQLSDWRD GVCTKYMQNC PKSQRYAYVV DACQPTCRGL SEADVTCSVS FVPVDGCTCP AGTFLNDAGA CVPAQECPCY AHGTVLAPGE VVHDEGAVCS CTGGKLSCLG ASLQKSTGCA APMVYLDCSN SSAGTPGAEC LRSCHTLDVG CFSTHCVSGC VCPPGLVSDG SGGCIAEEDC PCVHNEATYK PGETIRVDCN TCTCRNRRWE CSHRLCLGTC VAYGDGHFIT FDGDRYSFEG SCEYILAQDY CGDNTTHGTF RIVTENIPCG TTGTTCSKAI KLFVESYELI LQEGTFKAVA RGPGGDPPYK IRYMGIFLVI ETHGMAVSWD RKTSVFIRLH QDYKGRVCGL CGNFDDNAIN DFATRSRSVV GDALEFGNSW KLSPSCPDAL APKDPCTANP FRKSWAQKQC SILHGPTFAA CRSQVDSTKY YEACVNDACA CDSGGDCECF CTAVAAYAQA CHDAGLCVSW RTPDTCPLFC DFYNPHGGCE WHYQPCGAPC LKTCRNPSGH CLVDLPGLEG CYPKCPPSQP FFNEDQMKCV AQCGCYDKDG NYYDVGARVP TAENCQSCNC TPSGIQCAHS LEACTCTYED RTYSYQDVIY NTTDGLGACL IAICGSNGTI IRKAVACPGT PATTPFTFTT AWVPHSTTSP ALPVSTVCVR EVCRWSSWYN GHRPEPGLGG GDFETFENLR QRGYQVCPVL ADIECRAAQL PDMPLEELGQ QVDCDRMRGL MCANSQQSPP LCHDYELRVL CCEYVPCGPS HHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.45 mg/mL
BufferpH: 5.2 / Component - Concentration: 100.0 mM / Component - Formula: C6H13NO4S / Component - Name: MES
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88708
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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