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- PDB-9txk: Cryo-EM structure of active ITIH4N with 12A12 F(ab) -

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Basic information

Entry
Database: PDB / ID: 9txk
TitleCryo-EM structure of active ITIH4N with 12A12 F(ab)
Components
  • (12A12 mAb F(ab) ...) x 2
  • Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4
KeywordsIMMUNE SYSTEM / Protease inhibitor / plasma protein / complement / coagulation / contact cascade
Function / homology
Function and homology information


hyaluronan metabolic process / platelet dense granule lumen / endopeptidase inhibitor activity / acute-phase response / response to cytokine / serine-type endopeptidase inhibitor activity / Platelet degranulation / blood microparticle / extracellular matrix / extracellular exosome ...hyaluronan metabolic process / platelet dense granule lumen / endopeptidase inhibitor activity / acute-phase response / response to cytokine / serine-type endopeptidase inhibitor activity / Platelet degranulation / blood microparticle / extracellular matrix / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Inter-alpha-trypsin inhibitor heavy chain, C-terminal / : / Inter-alpha-trypsin inhibitor heavy chain C-terminus / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain ...Inter-alpha-trypsin inhibitor heavy chain, C-terminal / : / Inter-alpha-trypsin inhibitor heavy chain C-terminus / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Inter-alpha-trypsin inhibitor heavy chain H4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJoergensen, M.H. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF25OC0101234 Denmark
CitationJournal: To Be Published
Title: The plasma protease inhibitor ITIH4 forms oligomeric complexes and senses broader, proteolytic activity
Authors: Joergensen, M.H. / Andersen, G.R.
History
DepositionJan 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4
D: 12A12 mAb F(ab) heavy chain
E: 12A12 mAb F(ab) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8077
Polymers117,9163
Non-polymers8914
Water362
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

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Protein , 1 types, 1 molecules A

#1: Protein Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4 / ITI heavy chain H4 / ITI-HC4 / Inter-alpha-inhibitor heavy chain 4 / Inter-alpha-trypsin inhibitor ...ITI heavy chain H4 / ITI-HC4 / Inter-alpha-inhibitor heavy chain 4 / Inter-alpha-trypsin inhibitor family heavy chain-related protein / IHRP / Plasma kallikrein sensitive glycoprotein 120 / Gp120 / PK-120


Mass: 70018.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITIH4, IHRP, ITIHL1, PK120, PRO1851 / Production host: Homo sapiens (human) / References: UniProt: Q14624

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Antibody , 2 types, 2 molecules DE

#2: Antibody 12A12 mAb F(ab) heavy chain


Mass: 24204.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 12A12 mAb F(ab) light chain


Mass: 23693.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 3 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment with 12A12 F(ab)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2PHENIX1.21.2_5419model refinement
3EPU3.7image acquisition
13cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147648 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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