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- PDB-13bf: Cryo-EM structure of COL6A3-Fab complex -

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Basic information

Entry
Database: PDB / ID: 13bf
TitleCryo-EM structure of COL6A3-Fab complex
Components
  • Collagen alpha-3(VI) chain
  • Fab heavy chain
  • Fab light chain
KeywordsCELL ADHESION/Immune System / Extracellular matrix / Antigen antibody interaction / generative AI / de novo design / CELL ADHESION / CELL ADHESION-Immune System complex
Function / homology
Function and homology information


collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / Assembly of collagen fibrils and other multimeric structures / muscle organ development / Collagen degradation / ECM proteoglycans ...collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / Assembly of collagen fibrils and other multimeric structures / muscle organ development / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions / response to glucose / response to UV / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / sarcolemma / neuron apoptotic process / extracellular vesicle / extracellular matrix / cell adhesion / endoplasmic reticulum lumen / : / extracellular exosome / extracellular region
Similarity search - Function
Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain ...Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMedina, E. / Joseph, J.S. / Gowda, M. / Shanehsazzadeh, A. / Panwar, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Origin-1: a generative AI platform for de novo antibody design against novel epitopes
Authors: Levine, S. / Shanehsazzadeh, A.
History
DepositionApr 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 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

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
A: Collagen alpha-3(VI) chain


Theoretical massNumber of molelcules
Total (without water)56,5583
Polymers56,5583
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: Antibody Fab heavy chain


Mass: 23677.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab light chain


Mass: 23531.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Collagen alpha-3(VI) chain


Mass: 9349.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL6A3 / Production host: Homo sapiens (human) / References: UniProt: P12111
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: COL6A3-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 50 mM Tris pH 7.5, 300 mM NaCl
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: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.21rc1_5084model refinement
13RELION43D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 494000 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043816
ELECTRON MICROSCOPYf_angle_d0.785179
ELECTRON MICROSCOPYf_dihedral_angle_d5.56528
ELECTRON MICROSCOPYf_chiral_restr0.046568
ELECTRON MICROSCOPYf_plane_restr0.005664

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