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- EMDB-56404: ITIH4N:MASP-1cf:12A12 F(ab) 2:1:2 complex (Composite) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56404
TitleITIH4N:MASP-1cf:12A12 F(ab) 2:1:2 complex (Composite)
Map data
Sample
  • Complex: Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment in complex with MASP-1cf and 12A12 F(ab) in a 2:1:2 stoichiometry
    • Protein or peptide: Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4
    • Protein or peptide: Ligand glutamate from MASP-1cf
    • Protein or peptide: 12A12 mAb F(ab) heavy chain
    • Protein or peptide: 12A12 mAb F(ab) light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsProtease inhibitor / plasma protein / complement / coagulation / contact cascade / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJoergensen MH / Andersen GR
Funding support Denmark, 1 items
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 MH / Andersen GR
History
DepositionJan 15, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56404.png

Downloads & links

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Map

FileDownload / File: emd_56404.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.57 Å/pix.
x 256 pix.
= 401.92 Å		1.57 Å/pix.
x 256 pix.
= 401.92 Å		1.57 Å/pix.
x 256 pix.
= 401.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.0
Minimum - Maximum-29.736052000000001 - 62.030963999999997
Average (Standard dev.)-0.00026542018 (±1.0074738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 401.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment i...

EntireName: Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment in complex with MASP-1cf and 12A12 F(ab) in a 2:1:2 stoichiometry
Components
  • Complex: Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment in complex with MASP-1cf and 12A12 F(ab) in a 2:1:2 stoichiometry
    • Protein or peptide: Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4
    • Protein or peptide: Ligand glutamate from MASP-1cf
    • Protein or peptide: 12A12 mAb F(ab) heavy chain
    • Protein or peptide: 12A12 mAb F(ab) light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment i...

SupramoleculeName: Inter-alpha-trypsin inhibitor heavy chain 4 N-terminal fragment in complex with MASP-1cf and 12A12 F(ab) in a 2:1:2 stoichiometry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4

MacromoleculeName: Isoform 3 of Inter-alpha-trypsin inhibitor heavy chain H4
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.018852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EKNGIDIYSL TVDSRVSSRF AHTVVTSRVV NRANTVQEAT FQMELPKKAF ITNFSMIIDG MTYPGIIKEK AEAQAQYSAA VAKGKSAGL VKATGRNMEQ FQVSVSVAPN AKITFELVYE ELLKRRLGVY ELLLKVRPQQ LVKHLQMDIH IFEPQGISFL E TESTFMTN ...String:
EKNGIDIYSL TVDSRVSSRF AHTVVTSRVV NRANTVQEAT FQMELPKKAF ITNFSMIIDG MTYPGIIKEK AEAQAQYSAA VAKGKSAGL VKATGRNMEQ FQVSVSVAPN AKITFELVYE ELLKRRLGVY ELLLKVRPQQ LVKHLQMDIH IFEPQGISFL E TESTFMTN QLVDALTTWQ NKTKAHIRFK PTLSQQQKSP EQQETVLDGN LIIRYDVDRA ISGGSIQIEN GYFVHYFAPE GL TTMPKNV VFVIDKSGSM SGRKIQQTRE ALIKILDDLS PRDQFNLIVF STEATQWRPS LVPASAENVN KARSFAAGIQ ALG GTNIND AMLMAVQLLD SSNQEERLPE GSVSLIILLT DGDPTVGETN PRSIQNNVRE AVSGRYSLFC LGFGFDVSYA FLEK LALDN GGLARRIHED SDSALQLQDF YQEVANPLLT AVTFEYPSNA VEEVTQNNFR LLFKGSEMVV AGKLQDRGPD VLTAT VSGK LPTQNITFQT ESSVAEQEAE FQSPKYIFHN FMERLWAYLT IQQLLEQTVS ASDADQQALR NQALNLSLAY SFVTPL TSM VVTKPDDQEQ SQVAEKPMEG ESRNRNVHSA GAAGSRMNFR PGVLSSRQLG LPGPPDVPDH AAYHPFR

UniProtKB: Inter-alpha-trypsin inhibitor heavy chain H4

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Macromolecule #2: Ligand glutamate from MASP-1cf

MacromoleculeName: Ligand glutamate from MASP-1cf / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 289.285 Da
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AEA

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Macromolecule #3: 12A12 mAb F(ab) heavy chain

MacromoleculeName: 12A12 mAb F(ab) heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.204084 KDa
SequenceString: EVQLQQSGPE LVKPGASVKM SCKASGYTFK TYLMHWVKQK PGQGLEWIGY IDPYNDGTKY NEKFKGKATL TSDKSSSTAY MELSSLTSE DSAVYYCAKD YGYDTYWGQG TLVTVSAAKT TPPSVYPLAP GCGDTTGSSV TLGCLVKGYF PESVTVTWNS G SLSSSVHT ...String:
EVQLQQSGPE LVKPGASVKM SCKASGYTFK TYLMHWVKQK PGQGLEWIGY IDPYNDGTKY NEKFKGKATL TSDKSSSTAY MELSSLTSE DSAVYYCAKD YGYDTYWGQG TLVTVSAAKT TPPSVYPLAP GCGDTTGSSV TLGCLVKGYF PESVTVTWNS G SLSSSVHT FPALLQSGLY TMSSSVTVPS STWPSQTVTC SVAHPASSTT VDKKLEPSGP ISTINPCPP

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Macromolecule #4: 12A12 mAb F(ab) light chain

MacromoleculeName: 12A12 mAb F(ab) light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.693213 KDa
SequenceString: DIQMTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSTLHPDIPS RFSGSGSGRD YSFSISNLEP EDIATYYCL QYDNLWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIQMTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSTLHPDIPS RFSGSGSGRD YSFSISNLEP EDIATYYCL QYDNLWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 121186
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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