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- PDB-9man: Structure of Norrin in complex with human Tspan12 large extracell... -

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Basic information

Entry
Database: PDB / ID: 9man
TitleStructure of Norrin in complex with human Tspan12 large extracellular loop (Tspan12 LEL)
Components
  • Maltose/maltodextrin-binding periplasmic protein,Norrin
  • Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12
KeywordsSIGNALING PROTEIN / Complex
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 speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsXue, L. / Wang, Z. / Xu, W.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Norrin
B: Maltose/maltodextrin-binding periplasmic protein,Norrin
D: Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12
C: Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12


Theoretical massNumber of molelcules
Total (without water)223,9984
Polymers223,9984
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Norrin / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Norrie disease protein / X- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 55603.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 16-22 (ENLYFQG) in Chain A/B of Molecule 1 are TEV protease recognition/cut site
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, NDP, EVR2 / Production host: Homo sapiens (human) / References: UniProt: P0AEY0, UniProt: Q00604
#2: Protein Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Tspan-12 / Tetraspan NET-2 / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Tspan-12 / Tetraspan NET-2 / Transmembrane 4 superfamily member 12


Mass: 56395.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 106-112 (ENLYFQG) in Chain C/D of Molecule 2 are TEV protease recognition/cut site
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, TSPAN12, NET2, TM4SF12, UNQ774/PRO1568
Production host: Homo sapiens (human) / References: UniProt: P0AEY0, UniProt: O95859
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Norrin in complex with Tspan12 LEL / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212449 / Symmetry type: POINT

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