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- EMDB-74236: Cryo-EM structure of IGFBP7 dodecamer. The 3D refinement was focu... -

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Basic information

Entry
Database: EMDB / ID: EMD-74236
TitleCryo-EM structure of IGFBP7 dodecamer. The 3D refinement was focused on the central part of the dodecamer, which contains 12 IgC2 domains.
Map dataCryo-EM structure of IGFBP7 dodecamer. The 3D refinement was focused on the central part of the dodecamer, which contains 12 IgC2 domains.
Sample
  • Complex: Dodecameric complex of IGFBP7
    • Protein or peptide: Insulin-like growth factor-binding protein 7
KeywordsIGFBP7 / cell adhesion
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCai K / Zhang XW / Bai XC
Funding support United States, 1 items
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 XW / Bai XC
History
DepositionDec 3, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74236.png

Downloads & links

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Map

FileDownload / File: emd_74236.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of IGFBP7 dodecamer. The 3D refinement was focused on the central part of the dodecamer, which contains 12 IgC2 domains.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.32 Å		0.83 Å/pix.
x 320 pix.
= 264.32 Å		0.83 Å/pix.
x 320 pix.
= 264.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.012356331 - 0.027183566
Average (Standard dev.)0.00006047866 (±0.00074406463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of IGFBP7 dodecamer, half map 1....

Fileemd_74236_half_map_1.map
AnnotationCryo-EM structure of IGFBP7 dodecamer, half map 1. The 3D refinement was focused on the central part of the dodecamer, which contains 12 IgC2 domains.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of IGFBP7 dodecamer, half map 2....

Fileemd_74236_half_map_2.map
AnnotationCryo-EM structure of IGFBP7 dodecamer, half map 2. The 3D refinement was focused on the central part of the dodecamer, which contains 12 IgC2 domains.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dodecameric complex of IGFBP7

EntireName: Dodecameric complex of IGFBP7
Components
  • Complex: Dodecameric complex of IGFBP7
    • Protein or peptide: Insulin-like growth factor-binding protein 7

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Supramolecule #1: Dodecameric complex of IGFBP7

SupramoleculeName: Dodecameric complex of IGFBP7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Insulin-like growth factor-binding protein 7

MacromoleculeName: Insulin-like growth factor-binding protein 7 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.165381 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERPSLRALL LGAAGLLLLL LPLSSSSSSD TCGPCEPASC PPLPPLGCLL GETRDACGCC PMCARGEGEP CGGGGAGRGY CAPGMECVK SRKRRKGKAG AAAGGPGVSG VCVCKSRYPV CGSDGTTYPS GCQLRAASQR AESRGEKAIT QVSKGTCEQG P SIVTPPKD ...String:
MERPSLRALL LGAAGLLLLL LPLSSSSSSD TCGPCEPASC PPLPPLGCLL GETRDACGCC PMCARGEGEP CGGGGAGRGY CAPGMECVK SRKRRKGKAG AAAGGPGVSG VCVCKSRYPV CGSDGTTYPS GCQLRAASQR AESRGEKAIT QVSKGTCEQG P SIVTPPKD IWNVTGAQVY LSCEVIGIPT PVLIWNKVKR GHYGVQRTEL LPGDRDNLAI QTRGGPEKHE VTGWVLVSPL SK EDAGEYE CHASNSQGQA SASAKITVVD ALHEIPVKKG EGAEL

UniProtKB: Insulin-like growth factor-binding protein 7

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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

Concentration8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2961957
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Generated by RELION
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 26016
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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