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- PDB-9zhq: Cryo-EM structure of IGFBP7 dodecamer. -

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Basic information

Entry
Database: PDB / ID: 9zhq
TitleCryo-EM structure of IGFBP7 dodecamer.
ComponentsInsulin-like growth factor-binding protein 7
KeywordsCELL ADHESION / IGFBP7
Function / homology
Function and homology information


: / regulation of steroid biosynthetic process / response to cortisol / insulin-like growth factor binding / regulation of signal transduction / response to retinoic acid / embryo implantation / cellular response to hormone stimulus / Post-translational protein phosphorylation / regulation of cell growth ...: / regulation of steroid biosynthetic process / response to cortisol / insulin-like growth factor binding / regulation of signal transduction / response to retinoic acid / embryo implantation / cellular response to hormone stimulus / Post-translational protein phosphorylation / regulation of cell growth / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Senescence-Associated Secretory Phenotype (SASP) / cell adhesion / endoplasmic reticulum lumen / negative regulation of cell population proliferation / : / extracellular exosome / extracellular region
Similarity search - Function
Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. ...Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / Growth factor receptor cysteine-rich domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Insulin-like growth factor-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsCai, K. / Zhang, X.W. / Bai, X.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: IGFBP7 is a soluble cell adhesion molecule
Authors: Cai, K. / Zhang, X.W. / Bai, X.C.
History
DepositionDec 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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
C: Insulin-like growth factor-binding protein 7
D: Insulin-like growth factor-binding protein 7
E: Insulin-like growth factor-binding protein 7
F: Insulin-like growth factor-binding protein 7
G: Insulin-like growth factor-binding protein 7
H: Insulin-like growth factor-binding protein 7
I: Insulin-like growth factor-binding protein 7
J: Insulin-like growth factor-binding protein 7
K: Insulin-like growth factor-binding protein 7
L: Insulin-like growth factor-binding protein 7
M: Insulin-like growth factor-binding protein 7
N: Insulin-like growth factor-binding protein 7


Theoretical massNumber of molelcules
Total (without water)349,98512
Polymers349,98512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Insulin-like growth factor-binding protein 7 / IBP-7 / IGF-binding protein 7 / IGFBP-7 / IGFBP-rP1 / MAC25 protein / PGI2-stimulating factor / ...IBP-7 / IGF-binding protein 7 / IGFBP-7 / IGFBP-rP1 / MAC25 protein / PGI2-stimulating factor / Prostacyclin-stimulating factor / Tumor-derived adhesion factor / TAF


Mass: 29165.381 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGFBP7, MAC25, PSF / Production host: Homo sapiens (human) / References: UniProt: Q16270
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Dodecameric complex of IGFBP7 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 8 mg/ml / Embedding 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: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIX1.21.2_5419model refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2961957
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31657 / Symmetry type: POINT
RefinementHighest resolution: 4.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00321336
ELECTRON MICROSCOPYf_angle_d0.51628920
ELECTRON MICROSCOPYf_dihedral_angle_d10.248040
ELECTRON MICROSCOPYf_chiral_restr0.0423108
ELECTRON MICROSCOPYf_plane_restr0.0043900

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