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- EMDB-73374: Factor XIa in complex with Fab fragment of REGN9933-A2 -

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Basic information

Entry
Database: EMDB / ID: EMD-73374
TitleFactor XIa in complex with Fab fragment of REGN9933-A2
Map data
Sample
  • Complex: Factor XIa in complex with REGN9933-A2 Fab
    • Protein or peptide: Coagulation factor XI
    • Protein or peptide: REGN9933 Fab Heavy Chain
    • Protein or peptide: REGN9933 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCoagulation / protease / BLOOD CLOTTING
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / : / serine-type peptidase activity / blood coagulation / heparin binding / serine-type endopeptidase activity ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / : / serine-type peptidase activity / blood coagulation / heparin binding / serine-type endopeptidase activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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 ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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
Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSaotome K / Franklin MC
Funding support1 items
OrganizationGrant numberCountry
Other private
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
DepositionOct 17, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73374.png

Downloads & links

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Map

FileDownload / File: emd_73374.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. 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: 6.3
Minimum - Maximum-28.070677 - 51.106003000000001
Average (Standard dev.)-0.000000000003138 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73374_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73374_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Factor XIa in complex with REGN9933-A2 Fab

EntireName: Factor XIa in complex with REGN9933-A2 Fab
Components
  • Complex: Factor XIa in complex with REGN9933-A2 Fab
    • Protein or peptide: Coagulation factor XI
    • Protein or peptide: REGN9933 Fab Heavy Chain
    • Protein or peptide: REGN9933 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Factor XIa in complex with REGN9933-A2 Fab

SupramoleculeName: Factor XIa in complex with REGN9933-A2 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coagulation factor XI

MacromoleculeName: Coagulation factor XI / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: coagulation factor XIa
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.201125 KDa
SequenceString: MIFLYQVVHF ILFTSVSGEC VTQLLKDTCF EGGDITTVFT PSAKYCQVVC TYHPRCLLFT FTAESPSEDP TRWFTCVLKD SVTETLPRV NRTAAISGYS FKQCSHQISA CNKDIYVDLD MKGINYNSSV AKSAQECQER CTDDVHCHFF TYATRQFPSL E HRNICLLK ...String:
MIFLYQVVHF ILFTSVSGEC VTQLLKDTCF EGGDITTVFT PSAKYCQVVC TYHPRCLLFT FTAESPSEDP TRWFTCVLKD SVTETLPRV NRTAAISGYS FKQCSHQISA CNKDIYVDLD MKGINYNSSV AKSAQECQER CTDDVHCHFF TYATRQFPSL E HRNICLLK HTQTGTPTRI TKLDKVVSGF SLKSCALSNL ACIRDIFPNT VFADSNIDSV MAPDAFVCGR ICTHHPGCLF FT FFSQEWP KESQRNLCLL KTSESGLPST RIKKSKALSG FSLQSCRHSI PVFCHSSFYH DTDFLGEELD IVAAKSHEAC QKL CTNAVR CQFFTYTPAQ ASCNEGKGKC YLKLSSNGSP TKILHGRGGI SGYTLRLCKM DNECTTKIKP RIVGGTASVR GEWP WQVTL HTTSPTQRHL CGGSIIGNQW ILTAAHCFYG VESPKILRVY SGILNQSEIK EDTSFFGVQE IIIHDQYKMA ESGYD IALL KLETTVNYTD SQRPICLPSK GDRNVIYTDC WVTGWGYRKL RDKIQNTLQK AKIPLVTNEE CQKRYRGHKI THKMIC AGY REGGKDACKG DSGGPLSCKH NEVWHLVGIT SWGEGCAQRE RPGVYTNVVE YVDWILEKTQ AV

UniProtKB: Coagulation factor XI

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Macromolecule #2: REGN9933 Fab Heavy Chain

MacromoleculeName: REGN9933 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.587607 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFS NYAMNWVRQA PGKGLDWVSF IRSGGDTTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKV HPYTWDYGDA FDIWGQGTMV TVSSASTKGP SVFPLAPCSR STSESTAALG CLVKDYFPEP V TVSWNSGA ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS NYAMNWVRQA PGKGLDWVSF IRSGGDTTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKV HPYTWDYGDA FDIWGQGTMV TVSSASTKGP SVFPLAPCSR STSESTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTKTYTCNV DHKPSNTKVD KRVESKYGPP CPPCPAPEFL G

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Macromolecule #3: REGN9933 Light Chain

MacromoleculeName: REGN9933 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.438967 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 2.4 µm / Nominal defocus min: 1.4000000000000001 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: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 69006
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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