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- PDB-9w2b: Tspan-7 dimer in retraction fibers -

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Basic information

Entry
Database: PDB / ID: 9w2b
TitleTspan-7 dimer in retraction fibers
ComponentsTetraspanin-7
KeywordsMEMBRANE PROTEIN / Membrane curvature / cell protrusion
Function / homology
Function and homology information


Trafficking of GluR2-containing AMPA receptors / Cell surface interactions at the vascular wall / plasma membrane
Similarity search - Function
: / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.87 Å
AuthorsJia, X. / Wang, D.J. / Li, X.P. / Liu, N. / Yu, L. / Wang, H.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Vita / Year: 2026
Title: Polymerization of tetraspanin 7 into helical transmembrane skeletons for
Authors: Wang, D. / Jia, X. / Dharan, R. / Ren, J. / Zheng, Y. / Li, X. / Huang, M. / Xu, K. / Zhang, Q. / Sho, T. / Liu, S. / Yang, F. / Zhang, Q.C. / Sorkin, R. / Liu, N. / Wang, H.W. / Yu, L.
History
DepositionJul 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetraspanin-7
B: Tetraspanin-7


Theoretical massNumber of molelcules
Total (without water)55,3022
Polymers55,3022
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 Tetraspanin-7 / Tspan-7 / Cell surface glycoprotein A15 / Membrane component chromosome X surface marker 1 / T-cell ...Tspan-7 / Cell surface glycoprotein A15 / Membrane component chromosome X surface marker 1 / T-cell acute lymphoblastic leukemia-associated antigen 1 / TALLA-1 / Transmembrane 4 superfamily member 2


Mass: 27651.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSPAN7, A15, DXS1692E, MXS1, TM4SF2 / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P41732
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Tspan7 dimer in retraction fiber / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (Human) (human)
Source (recombinant)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 5.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1472338 / Symmetry type: POINT
RefinementHighest resolution: 5.87 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023952
ELECTRON MICROSCOPYf_angle_d0.5995370
ELECTRON MICROSCOPYf_dihedral_angle_d4.005536
ELECTRON MICROSCOPYf_chiral_restr0.041630
ELECTRON MICROSCOPYf_plane_restr0.003666

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