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- EMDB-41981: (Local hNBD1 Map) - "Mechanism of dual pharmacological correction... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41981
Title(Local hNBD1 Map) - "Mechanism of dual pharmacological correction and potentiation of human CFTR"
Map data
Sample
  • Complex: cystic fibrosis transmembrane conductance regulator(CFTR)
    • Protein or peptide: Human CFTR
Keywordscystic fibrosis transmembrane conductance regulator (CFTR) / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsHunt JF / Wang C / Singh S / Loughlin BJ / Yang Z / Xu H / Veit G / Vorobiev S / Clarke OB / Jiang F ...Hunt JF / Wang C / Singh S / Loughlin BJ / Yang Z / Xu H / Veit G / Vorobiev S / Clarke OB / Jiang F / Li Y / Rich Z / Menten ER / Grassucci RA / Wang W / Mezzell A / Fu Z / Wong K / Wetmore DR / Sutton RB / Brouillette CG / Urbatsch IL / Kappes JC / Lukacs GL / Frank J / Cohen BM
Funding support United States, 6 items
OrganizationGrant numberCountry
Cystic Fibrosis FoundationHunt18G0 United States
Cystic Fibrosis FoundationHunt20G0 United States
Cystic Fibrosis FoundationHUNT13XX0 United States
Cystic Fibrosis Foundation004400G222 United States
Cystic Fibrosis FoundationFRANK16XX0 United States
Cystic Fibrosis FoundationFRANK18G0 United States
CitationJournal: To Be Published
Title: Mechanism of dual pharmacological correction and potentiation of human CFTR
Authors: Wang C / Yang Z / Loughlin BJ / Xu H / Veit G / Vorobiev S / Clarke OB / Jiang F / Li Y / Singh S / Rich Z / Menten ER / Grassucci RA / Wang W / Mezzell A / Fu Z / Wong K / Wetmore DR / ...Authors: Wang C / Yang Z / Loughlin BJ / Xu H / Veit G / Vorobiev S / Clarke OB / Jiang F / Li Y / Singh S / Rich Z / Menten ER / Grassucci RA / Wang W / Mezzell A / Fu Z / Wong K / Wetmore DR / Sutton RB / Brouillette CG / Urbatsch IL / Kappes JC / Lukacs GL / Frank J / Hunt JF / Cohen BM
History
DepositionSep 15, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41981.png

Downloads & links

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Map

FileDownload / File: emd_41981.map.gz / Format: CCP4 / Size: 125 MB / 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 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.066
Minimum - Maximum-0.32768077 - 0.84747446
Average (Standard dev.)0.0014090048 (±0.013132374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41981_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_41981_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 : cystic fibrosis transmembrane conductance regulator(CFTR)

EntireName: cystic fibrosis transmembrane conductance regulator(CFTR)
Components
  • Complex: cystic fibrosis transmembrane conductance regulator(CFTR)
    • Protein or peptide: Human CFTR

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Supramolecule #1: cystic fibrosis transmembrane conductance regulator(CFTR)

SupramoleculeName: cystic fibrosis transmembrane conductance regulator(CFTR)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Human CFTR

MacromoleculeName: Human CFTR / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GGSQRSPLEK ASVVSKLFFS WTRPILRKGY RQRLELSDIY QIPSVDSADN LSEKLEREWD RELASKKNPK LINALRRCFF WRFMFYGIFL YLGEVTKAVQ PLLLGRIIAS YDPDNKEERS IAIYLGIGLC LLFIVRTLLL HPAIFGLHHI GMQMRIAMFS LIYKKTLKLS ...String:
GGSQRSPLEK ASVVSKLFFS WTRPILRKGY RQRLELSDIY QIPSVDSADN LSEKLEREWD RELASKKNPK LINALRRCFF WRFMFYGIFL YLGEVTKAVQ PLLLGRIIAS YDPDNKEERS IAIYLGIGLC LLFIVRTLLL HPAIFGLHHI GMQMRIAMFS LIYKKTLKLS SRVLDKISIG QLVSLLSNNL NKFDEGLALA HFVWIAPLQV ALLMGLIWEL LQASAFCGLG FLIVLALFQA GLGRMMMKYR DQRAGKISER LVITSEMIEN IQSVKAYCWE EAMEKMIENL RQTELKLTRK AAYVRYFNSS AFFFSGFFVV FLSVLPYALI KGIILRKIFT TISFCIVLRM AVTRQFPWAV QTWYDSLGAI NKIQDFLQKQ EYKTLEYNLT TTEVVMENVT AFWEEGGTPV LKDINFKIER GQLLAVAGST GAGKTSLLMV IMGELEPSEG KIKHSGRISF CPQFPWIMPG TIKENIIFGV SYDEYRYRSV IKACQLEEDI SKFPEKDNTV LGEGGITLSG DQRAKISLAR AVYKDADLYL LDSPFGYLDV LTEKEIFESC VCKLMANKTR ILVTSKMEHL KKADKILILH EGSSYFYGTF SELQNLQPDF SSKLMGCDSF DQFSAERRNS ILTETLHRFS LEGDAPVSWT ETKKQSFKQT GEFGEKRKNS ILNPINSIRK FSIVQKTPLQ MNGIEEDSDE PLERRLSLVP DSEQGEAILP RISVISTGPT LQARRRQSVL NLMTHSVNQG QNIHRKTTAS TRKVSLAPQA NLTELDIYSR RLSQETGLEI SEEINEEDLK ECFFDDMESI PAVTTWNTYL RYITVHKSLI FVLIWCLVIF LAEVAASLVV LWLLGNTPLQ DKGNSTHSRN NSYAVIITST SSYYVFYIYV GVADTLLAMG FFRGLPLVHT LITVSKILHH KMLHSVLQAP MSTLNTLKAG GILNRFSKDI AILDDLLPLT IFDFIQLLLI VIGAIAVVAV LQPYIFVATV PVIVAFIMLR AYFLQTSQQL KQLESEGRSP IFTHLVTSLK GLWTLRAFGR QPYFETLFHK ALNLHTANWF LYLSTLRWFQ MRIEMIFVIF FIAVTFISIL TTGEGEGRVG IILTLAMNIM STLQWAVNSS IDVDSLMRSV SRVFKFIDMP TEGKPTKSTK PYKNGQLSKV MIIENSHVKK DDIWPSGGQM TVKDLTAKYT EGGNAILENI SFSISPGQRV GLLGRTGSGK STLLSAFLRL LNTEGEIQID GVSWDSITLQ QWRKAFGVIP QKVFIFSGTF RKNLDPYEQW SDQEIWKVAD EVGLRSVIEQ FPGKLDFVLV DGGCVLSHGH KQLMCLARSV LSKAKILLLD EPSAHLDPVT YQIIRRTLKQ AFADCTVILC EHRIEAMLEC QQFLVIEENK VRQYDSIQKL LNERSLFRQA ISPSDRVKLF PHRNSSKCKS KPQIAALKEE TEEEVQDTRL LEENLYFQ

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.45 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5w81

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127136
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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