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- EMDB-49728: TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-49728
TitleTMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab
Map data
Sample
  • Complex: TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab
    • Protein or peptide: Transmembrane protease serine 6
    • Protein or peptide: REGN7999 Fab light chain
    • Protein or peptide: REGN7999 Fab heavy chain
    • Protein or peptide: REGN8023 Fab light chain
    • Protein or peptide: REGN8023 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsSerine protease / Matriptase / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane protein proteolysis / self proteolysis / Collagen degradation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / negative regulation of BMP signaling pathway / extracellular matrix disassembly / BMP signaling pathway / Degradation of the extracellular matrix / metalloendopeptidase activity ...membrane protein proteolysis / self proteolysis / Collagen degradation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / negative regulation of BMP signaling pathway / extracellular matrix disassembly / BMP signaling pathway / Degradation of the extracellular matrix / metalloendopeptidase activity / multicellular organismal-level iron ion homeostasis / intracellular iron ion homeostasis / serine-type endopeptidase activity / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
Similarity search - Function
Peptidase S1A, matriptase-2 / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / LDL-receptor class A (LDLRA) domain signature. ...Peptidase S1A, matriptase-2 / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSaotome K / Franklin MC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 14, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49728.png

Downloads & links

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Map

FileDownload / File: emd_49728.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0162
Minimum - Maximum-0.12970822 - 0.23184638
Average (Standard dev.)0.000022760507 (±0.0031221935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49728_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49728_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab

EntireName: TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab
Components
  • Complex: TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab
    • Protein or peptide: Transmembrane protease serine 6
    • Protein or peptide: REGN7999 Fab light chain
    • Protein or peptide: REGN7999 Fab heavy chain
    • Protein or peptide: REGN8023 Fab light chain
    • Protein or peptide: REGN8023 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab

SupramoleculeName: TMPRSS6 in complex with REGN7999 Fab and REGN8023 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transmembrane protease serine 6

MacromoleculeName: Transmembrane protease serine 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.15482 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: GYKAEVMVSQ VYSGSLRVLN RHFSQDLTRR ESSAFRSETA KAQKMLKELI TSTRLGTYYN SSSVYSFGEG PLTCFFWFIL QIPEHRRLM LSPEVVQALL VEELLSTVNS SAAVPYRAEY EVDPEGLVIL EASVKDIAAL NSTLGCYRYS YVGQGQVLRL K GPDHLASS ...String:
GYKAEVMVSQ VYSGSLRVLN RHFSQDLTRR ESSAFRSETA KAQKMLKELI TSTRLGTYYN SSSVYSFGEG PLTCFFWFIL QIPEHRRLM LSPEVVQALL VEELLSTVNS SAAVPYRAEY EVDPEGLVIL EASVKDIAAL NSTLGCYRYS YVGQGQVLRL K GPDHLASS CLWHLQGPKD LMLKLRLEWT LAECRDRLAM YDVAGPLEKR LITSVYGCSR QEPVVEVLAS GAIMAVVWKK GL HSYYDPF VLSVQPVVFQ ACEVNLTLDN RLDSQGVLST PYFPSYYSPQ THCSWHLTVP SLDYGLALWF DAYALRRQKY DLP CTQGQW TIQNRRLCGL RILQPYAERI PVVATAGITI NFTSQISLTG PGVRVHYGLY NQSDPCPGEF LCSVNGLCVP ACDG VKDCP NGLDERNCVC RATFQCKEDS TCISLPKVCD GQPDCLNGSD EEQCQEGVPC GTFTFQCEDR SCVKKPNPQC DGRPD CRDG SDEEHCDCGL QGPSSRIVGG AVSSEGEWPW QASLQVRGRH ICGGALIADR WVITAAHCFQ EDSMASTVLW TVFLGK VWQ NSRWPGEVSF KVSRLLLHPY HEEDSHDYDV ALLQLDHPVV RSAAVRPVCL PARSHFFEPG LHCWITGWGA LREGGPI SN ALQKVDVQLI PQDLCSEVYR YQVTPRMLCA GYRKGKKDAC QGDAGGPLVC KALSGRWFLA GLVSWGLGCG RPNYFGVY T RITGVISWIQ QVVTEQKLIS EEDLGGEQKL ISEEDLHHHH HH

UniProtKB: Transmembrane protease serine 6

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Macromolecule #2: REGN7999 Fab light chain

MacromoleculeName: REGN7999 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.381912 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASVGDRVI ITCRASQDFN SWLAWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QTDSFPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVI ITCRASQDFN SWLAWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QTDSFPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: REGN7999 Fab heavy chain

MacromoleculeName: REGN7999 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.604521 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMTWVRQA PGKGLEWVSA ISGSDTSTYY ADSVKGRFTI SRDNSKNTLF LQMNSLRAE DTAVYYCAKH QDYDFSYYYS AMDVWGQGTT VTVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMTWVRQA PGKGLEWVSA ISGSDTSTYY ADSVKGRFTI SRDNSKNTLF LQMNSLRAE DTAVYYCAKH QDYDFSYYYS AMDVWGQGTT VTVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTKTYTCN VDHKPSNTKV DKRVESKYGP PCPPCPAPEF LG

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Macromolecule #4: REGN8023 Fab light chain

MacromoleculeName: REGN8023 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.117859 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL DSDDGNTYLD WYLRKPGQSP QLLIYTLSYR ASGVPDRFSG SGSGTDFTLK ISRVEADDV GVYYCMQRIE FPLTFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL DSDDGNTYLD WYLRKPGQSP QLLIYTLSYR ASGVPDRFSG SGSGTDFTLK ISRVEADDV GVYYCMQRIE FPLTFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #5: REGN8023 Fab heavy chain

MacromoleculeName: REGN8023 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.308553 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVKPGGSLRI SCAASGFIFV DYAMHWVRQA PGKGLEWVSG ISWNSGSIGY ADSVKGRFTI SRDNAKKSLY LQMSGLRPE DTALYYCVKS GFYYVRSYFD NWGQGTLVTV SSASTKGPSV FPLAPCSRST SESTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLVESGGG LVKPGGSLRI SCAASGFIFV DYAMHWVRQA PGKGLEWVSG ISWNSGSIGY ADSVKGRFTI SRDNAKKSLY LQMSGLRPE DTALYYCVKS GFYYVRSYFD NWGQGTLVTV SSASTKGPSV FPLAPCSRST SESTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TKTYTCNVDH KPSNTKVDKR VESKYGPPCP PCPAPEFLG

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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: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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
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: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105142
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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