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- EMDB-63756: Structure of Norrin in complex with human Tspan12 large extracell... -

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Basic information

Entry
Database: EMDB / ID: EMD-63756
TitleStructure of Norrin in complex with human Tspan12 large extracellular loop (Tspan12 LEL)
Map data
Sample
  • Complex: Norrin in complex with Tspan12 LEL
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Norrin
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12
KeywordsComplex / SIGNALING PROTEIN
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / retinal rod cell differentiation / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / glycine metabolic process / retina layer formation / retinal pigment epithelium development ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / retinal rod cell differentiation / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / glycine metabolic process / retina layer formation / retinal pigment epithelium development / endothelial cell differentiation / microglial cell proliferation / dendritic spine development / establishment of blood-retinal barrier / vacuole organization / microglia differentiation / protein targeting to lysosome / establishment of blood-brain barrier / frizzled binding / optic nerve development / retinal ganglion cell axon guidance / lens development in camera-type eye / ubiquitin-dependent endocytosis / smoothened signaling pathway / maintenance of blood-brain barrier / exploration behavior / decidualization / action potential / carbohydrate transmembrane transporter activity / maltose binding / regulation of angiogenesis / maltose transport / maltodextrin transmembrane transport / blood vessel remodeling / canonical Wnt signaling pathway / response to axon injury / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / tricarboxylic acid cycle / visual perception / transforming growth factor beta receptor signaling pathway / cytokine activity / glutathione metabolic process / nervous system development / mitotic cell cycle / outer membrane-bounded periplasmic space / neuron apoptotic process / angiogenesis / cellular response to hypoxia / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / inflammatory response / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / : / membrane / plasma membrane
Similarity search - Function
Norrie disease protein / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. ...Norrie disease protein / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine-knot cytokine / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Tetraspanin-12 / Maltose/maltodextrin-binding periplasmic protein / Norrin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsXue L / Wang Z / Xu W
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030302 China
CitationJournal: To Be Published
Title: Structure of Norrin in complex with human Tspan12 large extracellular loop (Tspan12 LEL)
Authors: Xue L / Wang Z / Xu W
History
DepositionMar 14, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63756.png

Downloads & links

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Map

FileDownload / File: emd_63756.map.gz / Format: CCP4 / Size: 669.9 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 560 pix.
= 465.92 Å		0.83 Å/pix.
x 560 pix.
= 465.92 Å		0.83 Å/pix.
x 560 pix.
= 465.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0641
Minimum - Maximum-0.286425 - 0.5741886
Average (Standard dev.)0.0008137528 (±0.01626919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 465.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63756_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: #1

Fileemd_63756_additional_1.map
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Histogram

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Half map: #2

Fileemd_63756_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63756_half_map_2.map
Projections & Slices
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Sample components

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Entire : Norrin in complex with Tspan12 LEL

EntireName: Norrin in complex with Tspan12 LEL
Components
  • Complex: Norrin in complex with Tspan12 LEL
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Norrin
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12

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Supramolecule #1: Norrin in complex with Tspan12 LEL

SupramoleculeName: Norrin in complex with Tspan12 LEL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Norrin

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Norrin
type: protein_or_peptide / ID: 1
Details: Residues 16-22 (ENLYFQG) in Chain A/B of Molecule 1 are TEV protease recognition/cut site
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.603055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSHHHHHHHH MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF ...String:
GSHHHHHHHH MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NG PWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYE EELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTNAAAENLY FQGEFKTDSS FIMD SDPRR CMRHHYVDSI SHPLYKCSSK MVLLARCEGH CSQASRSEPL VSFSTVLKQP FRSSCHCCRP QTSKLKALRL RCSGG MRLT ATYRYILSCH CEECNS

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Norrin

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12
type: protein_or_peptide / ID: 2
Details: Residues 106-112 (ENLYFQG) in Chain C/D of Molecule 2 are TEV protease recognition/cut site
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.395746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSHHHHHHHH MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF ...String:
GSHHHHHHHH MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NG PWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYE EELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTNAAAENLY FQGEFYEQEL MVPV QWSDM VTLKARMTNY GLPRYRWLTH AWNFFQREFK CCGVVYFTDW LEMTEMDWPP DSCCVREFPG CSKQAHQEDL SDLYQ EGCG KKMYSFLRGT KQLQVLR

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Tetraspanin-12

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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

Concentration1.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212449
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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