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- EMDB-43969: Structure of the semi-extended AlphaIIbBeta3 in complex with R21D... -

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Basic information

Entry
Database: EMDB / ID: EMD-43969
TitleStructure of the semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
Map datathis is the main map.
Sample
  • Complex: The semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
    • Protein or peptide: Integrin alpha-IIb
    • Protein or peptide: Integrin beta-3
    • Protein or peptide: R21D10 Fab heavy chain
    • Protein or peptide: R21D10 Fab light chain
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsmonoclonal antibody / integrin receptor / allosteric inhibitor / platelets / BLOOD CLOTTING / BLOOD CLOTTING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / Signaling by RAF1 mutants
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang JL / Walz T / Coller B / Wang L / Li JH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL019278-48 United States
CitationJournal: Blood Adv / Year: 2024
Title: An αIIbβ3 monoclonal antibody traps a semiextended conformation and allosterically inhibits large ligand binding.
Authors: Lu Wang / Jialing Wang / Jihong Li / Thomas Walz / Barry S Coller /
Abstract: Monoclonal antibodies (mAbs) have provided valuable information regarding the structure and function of platelet αIIbβ3. Protein disulfide isomerase (PDI) has been implicated in αIIbβ3 activation ...Monoclonal antibodies (mAbs) have provided valuable information regarding the structure and function of platelet αIIbβ3. Protein disulfide isomerase (PDI) has been implicated in αIIbβ3 activation and binds to thrombin-activated αIIbβ3. Using human platelets as the immunogen, we identified a new mAb (R21D10) that inhibits the binding of PDI to platelets activated with thrombin receptor-activating peptide (T6). R21D10 also partially inhibited T6-induced fibrinogen and PAC-1 binding to platelets, as well as T6- and adenosine 5'-diphosphate-induced platelet aggregation. Mutual competition experiments showed that R21D10 does not inhibit the binding of mAbs 10E5 (anti-αIIb cap domain) or 7E3 (anti-β3 β-I domain), and immunoblot studies indicated that R21D10 binds to β3. The dissociation of αIIbβ3 by EDTA had a minimal effect on R21D10 binding. Cryogenic electron microscopy of the αIIbβ3-R21D10 Fab complex revealed that R21D10 binds to the β3 integrin-epidermal growth factor 1 (I-EGF1) domain and traps an intermediate conformation of αIIbβ3 with semiextended leg domains. The binding of R21D10 produces a major structural change in the β3 I-EGF2 domain associated with a new interaction between the β3 I-EGF2 and αIIb thigh domains, which may prevent the swing-out motion of the β3 hybrid domain required for high-affinity ligand binding and protect αIIbβ3 from EDTA-induced dissociation. R21D10 partially reversed the ligand binding priming effect of eptifibatide, suggesting that it could convert the swung-out conformation into a semiextended conformation. We concluded that R21D10 inhibits ligand binding to αIIbβ3 via a unique allosteric mechanism, which may or may not be related to its inhibition of PDI binding.
History
DepositionMar 6, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43969.png

Downloads & links

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Map

FileDownload / File: emd_43969.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is the main map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-5.099675 - 6.23122
Average (Standard dev.)0.000119833145 (±0.08704404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: this is half B map.

Fileemd_43969_half_map_1.map
Annotationthis is half B map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: this is half A map.

Fileemd_43969_half_map_2.map
Annotationthis is half A 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 : The semi-extended AlphaIIbBeta3 in complex with R21D10 Fab

EntireName: The semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
Components
  • Complex: The semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
    • Protein or peptide: Integrin alpha-IIb
    • Protein or peptide: Integrin beta-3
    • Protein or peptide: R21D10 Fab heavy chain
    • Protein or peptide: R21D10 Fab light chain
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: The semi-extended AlphaIIbBeta3 in complex with R21D10 Fab

SupramoleculeName: The semi-extended AlphaIIbBeta3 in complex with R21D10 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Integrin alpha-IIb

MacromoleculeName: Integrin alpha-IIb / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.477523 KDa
SequenceString: MARALCPLQA LWLLEWVLLL LGPCAAPPAW ALNLDPVQLT FYAGPNGSQF GFSLDFHKDS HGRVAIVVGA PRTLGPSQEE TGGVFLCPW RAEGGQCPSL LFDLRDETRN VGSQTLQTFK ARQGLGASVV SWSDVIVACA PWQHWNVLEK TEEAEKTPVG S CFLAQPES ...String:
MARALCPLQA LWLLEWVLLL LGPCAAPPAW ALNLDPVQLT FYAGPNGSQF GFSLDFHKDS HGRVAIVVGA PRTLGPSQEE TGGVFLCPW RAEGGQCPSL LFDLRDETRN VGSQTLQTFK ARQGLGASVV SWSDVIVACA PWQHWNVLEK TEEAEKTPVG S CFLAQPES GRRAEYSPCR GNTLSRIYVE NDFSWDKRYC EAGFSSVVTQ AGELVLGAPG GYYFLGLLAQ APVADIFSSY RP GILLWHV SSQSLSFDSS NPEYFDGYWG YSVAVGEFDG DLNTTEYVVG APTWSWTLGA VEILDSYYQR LHRLRGEQMA SYF GHSVAV TDVNGDGRHD LLVGAPLYME SRADRKLAEV GRVYLFLQPR GPHALGAPSL LLTGTQLYGR FGSAIAPLGD LDRD GYNDI AVAAPYGGPS GRGQVLVFLG QSEGLRSRPS QVLDSPFPTG SAFGFSLRGA VDIDDNGYPD LIVGAYGANQ VAVYR AQPV VKASVQLLVQ DSLNPAVKSC VLPQTKTPVS CFNIQMCVGA TGHNIPQKLS LNAELQLDRQ KPRQGRRVLL LGSQQA GTT LNLDLGGKHS PICHTTMAFL RDEADFRDKL SPIVLSLNVS LPPTEAGMAP AVVLHGDTHV QEQTRIVLDC GEDDVCV PQ LQLTASVTGS PLLVGADNVL ELQMDAANEG EGAYEAELAV HLPQGAHYMR ALSNVEGFER LICNQKKENE TRVVLCEL G NPMKKNAQIG IAMLVSVGNL EEAGESVSFQ LQIRSKNSQN PNSKIVLLDV PVRAEAQVEL RGNSFPASLV VAAEEGERE QNSLDSWGPK VEHTYELHNN GPGTVNGLHL SIHLPGQSQP SDLLYILDIQ PQGGLQCFPQ PPVNPLKVDW GLPIPSPSPI HPAHHKRDR RQIFLPEPEQ PSRLQDPVLV SCDSAPCTVV QCDLQEMARG QRAMVTVLAF LWLPSLYQRP LDQFVLQSHA W FNVSSLPY AVPPLSLPRG EAQVWTQLLR ALEERAIPIW WVLVGVLGGL LLLTILVLAM WKVGFFKRNR PPLEEDDEEG E

UniProtKB: Integrin alpha-IIb

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Macromolecule #2: Integrin beta-3

MacromoleculeName: Integrin beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.150773 KDa
SequenceString: MRARPRPRPL WATVLALGAL AGVGVGGPNI CTTRGVSSCQ QCLAVSPMCA WCSDEALPLG SPRCDLKENL LKDNCAPESI EFPVSEARV LEDRPLSDKG SGDSSQVTQV SPQRIALRLR PDDSKNFSIQ VRQVEDYPVD IYYLMDLSYS MKDDLWSIQN L GTKLATQM ...String:
MRARPRPRPL WATVLALGAL AGVGVGGPNI CTTRGVSSCQ QCLAVSPMCA WCSDEALPLG SPRCDLKENL LKDNCAPESI EFPVSEARV LEDRPLSDKG SGDSSQVTQV SPQRIALRLR PDDSKNFSIQ VRQVEDYPVD IYYLMDLSYS MKDDLWSIQN L GTKLATQM RKLTSNLRIG FGAFVDKPVS PYMYISPPEA LENPCYDMKT TCLPMFGYKH VLTLTDQVTR FNEEVKKQSV SR NRDAPEG GFDAIMQATV CDEKIGWRND ASHLLVFTTD AKTHIALDGR LAGIVQPNDG QCHVGSDNHY SASTTMDYPS LGL MTEKLS QKNINLIFAV TENVVNLYQN YSELIPGTTV GVLSMDSSNV LQLIVDAYGK IRSKVELEVR DLPEELSLSF NATC LNNEV IPGLKSCMGL KIGDTVSFSI EAKVRGCPQE KEKSFTIKPV GFKDSLIVQV TFDCDCACQA QAEPNSHRCN NGNGT FECG VCRCGPGWLG SQCECSEEDY RPSQQDECSP REGQPVCSQR GECLCGQCVC HSSDFGKITG KYCECDDFSC VRYKGE MCS GHGQCSCGDC LCDSDWTGYY CNCTTRTDTC MSSNGLLCSG RGKCECGSCV CIQPGSYGDT CEKCPTCPDA CTFKKEC VE CKKFDRGALH DENTCNRYCR DEIESVKELK DTGKDAVNCT YKNEDDCVVR FQYYEDSSGK SILYVVEEPE CPKGPDIL V VLLSVMGAIL LIGLAALLIW KLLITIHDRK EFAKFEEERA RAKWDTANNP LYKEATSTFT NITYRGT

UniProtKB: Integrin beta-3

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Macromolecule #3: R21D10 Fab heavy chain

MacromoleculeName: R21D10 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.539334 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVQLQESGAE LAKPGASVKM SCKASGYTFT DYWMHWVKQR PGQGLEWIGY INPSTGYTEY NQKFKDKATL TADKSSSTAY MQLSSLTSE DSAVYYCARW RGVYRSDVHY YAMDYWGQGT SVTVSSAKTT APSVYPLAPV CGDTTGSSVT LGCLVKGYFP E PVTLTWNS ...String:
EVQLQESGAE LAKPGASVKM SCKASGYTFT DYWMHWVKQR PGQGLEWIGY INPSTGYTEY NQKFKDKATL TADKSSSTAY MQLSSLTSE DSAVYYCARW RGVYRSDVHY YAMDYWGQGT SVTVSSAKTT APSVYPLAPV CGDTTGSSVT LGCLVKGYFP E PVTLTWNS GSLSSGVHTF PAVLQSDLYT LSSSVTVTSS AAPSQSITCN VAHPASSTKV DKKIEPRGP

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Macromolecule #4: R21D10 Fab light chain

MacromoleculeName: R21D10 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.344779 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QIVLTQSPAI MSASPGEKVT MTCSASSSVS YMHWYQQKSG TSPKRWIYDT SKLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSKPPTFGA GTKLELKWAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
QIVLTQSPAI MSASPGEKVT MTCSASSSVS YMHWYQQKSG TSPKRWIYDT SKLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSKPPTFGA GTKLELKWAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 7 / 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

Concentration0.05 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1332000
Startup modelType of model: OTHER
Details: generate initial model based on selected averages of particles after 2D-classification in CryoSPARC.
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.0) / Number images used: 596272
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.4.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 183000 / Software - Name: cryoSPARC (ver. v4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3fsc

chain_id: A, source_name: PDB, initial_model_type: experimental model

3fsc

chain_id: B, source_name: PDB, initial_model_type: experimental model

7la4

chain_id: H, source_name: PDB, initial_model_type: experimental model

7la4

chain_id: L, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9axl:
Structure of the semi-extended AlphaIIbBeta3 in complex with R21D10 Fab

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