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- PDB-6djp: Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68 -

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Basic information

Entry
Database: PDB / ID: 6djp
TitleIntegrin alpha-v beta-8 in complex with the Fabs 8B8 and 68
Components
  • 68 heavy chain Fab
  • 68 light chain Fab
  • 8B8 heavy chain Fab
  • 8B8 light chain Fab
  • Integrin alpha-v
  • Integrin beta-8
KeywordsMEMBRANE PROTEIN / GLYCOPROTEIN / ADHESION / FAB
Function / homology
Function and homology information


placenta blood vessel development / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding ...placenta blood vessel development / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / Laminin interactions / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / positive regulation of small GTPase mediated signal transduction / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / cartilage development / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / negative regulation of low-density lipoprotein particle clearance / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / endodermal cell differentiation / negative chemotaxis / positive regulation of osteoblast proliferation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / cell-substrate adhesion / microvillus membrane / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / positive regulation of intracellular signal transduction / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / vasculogenesis / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / ECM proteoglycans / Integrin cell surface interactions / specific granule membrane / coreceptor activity / substrate adhesion-dependent cell spreading / phagocytic vesicle / cell-matrix adhesion / positive regulation of cell adhesion / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of extrinsic apoptotic signaling pathway / protein kinase C binding / Signal transduction by L1 / cell-cell adhesion / VEGFA-VEGFR2 Pathway / integrin binding / ruffle membrane / calcium ion transmembrane transport / positive regulation of angiogenesis / cell migration / positive regulation of cytosolic calcium ion concentration / virus receptor activity / signaling receptor activity / angiogenesis / protease binding / cell adhesion / positive regulation of cell migration / negative regulation of gene expression / external side of plasma membrane / focal adhesion / positive regulation of gene expression / positive regulation of cell population proliferation / Neutrophil degranulation / symbiont entry into host cell / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Teneurin-like EGF domain / : / Integrin alpha Ig-like domain 3 / : / Integrin EGF domain / EGF-like domain / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain ...Teneurin-like EGF domain / : / Integrin alpha Ig-like domain 3 / : / Integrin EGF domain / EGF-like domain / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / 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, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Integrin alpha-V / Integrin beta-8
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsCormier, A. / Campbell, M.G. / Nishimura, S.L. / Cheng, Y.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54HL119893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01HL113032 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01HL134183 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41CA196276 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM structure of the αvβ8 integrin reveals a mechanism for stabilizing integrin extension.
Authors: Anthony Cormier / Melody G Campbell / Saburo Ito / Shenping Wu / Jianlong Lou / James Marks / Jody L Baron / Stephen L Nishimura / Yifan Cheng /
Abstract: Integrins are conformationally flexible cell surface receptors that survey the extracellular environment for their cognate ligands. Interactions with ligands are thought to be linked to global ...Integrins are conformationally flexible cell surface receptors that survey the extracellular environment for their cognate ligands. Interactions with ligands are thought to be linked to global structural rearrangements involving transitions between bent, extended-closed and extended-open forms. Thus far, structural details are lacking for integrins in the extended conformations due to extensive flexibility between the headpiece and legs in this conformation. Here we present single-particle electron cryomicroscopy structures of human αvβ8 integrin in the extended-closed conformation, which has been considered to be a low-affinity intermediate. Our structures show the headpiece rotating about a flexible αv knee, suggesting a ligand surveillance mechanism for integrins in their extended-closed form. Our model predicts that the extended conformation is mainly stabilized by an interface formed between flexible loops in the upper and lower domains of the αv leg. Confirming these findings with the αvβ3 integrin suggests that our model of stabilizing the extended-closed conformation is generalizable to other integrins.
History
DepositionMay 25, 2018Deposition site: RCSB / Processing site: RCSB
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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Integrin alpha-v
B: Integrin beta-8
C: 8B8 heavy chain Fab
D: 8B8 light chain Fab
E: 68 heavy chain Fab
F: 68 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,90116
Polymers270,2536
Non-polymers4,64810
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-v / Vitronectin receptor / Vitronectin receptor subunit alpha


Mass: 106758.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Cell line (production host): CHO lec 3.2.8.1 / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06756
#2: Protein Integrin beta-8


Mass: 70837.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB8 / Cell line (production host): CHO lec 3.2.8.1 / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P26012

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Antibody , 4 types, 4 molecules CDEF

#3: Antibody 8B8 heavy chain Fab


Mass: 23314.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#4: Antibody 8B8 light chain Fab


Mass: 23241.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#5: Antibody 68 heavy chain Fab


Mass: 22680.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#6: Antibody 68 light chain Fab


Mass: 23420.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 4 types, 10 molecules

#7: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(4+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#10: 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: isolated from a genetically manipulated source
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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Details

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: Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.312 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 6.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 6 sec. / Electron dose: 41 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 713
Image scansMovie frames/image: 30

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
7PHENIXmodel fitting
9RELIONinitial Euler assignment
10FREALIGN9.11final Euler assignment
11RELIONclassification
12FREALIGN9.113D reconstruction
13Rosettamodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17442 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00711586
ELECTRON MICROSCOPYf_angle_d1.16215765
ELECTRON MICROSCOPYf_dihedral_angle_d6.8216822
ELECTRON MICROSCOPYf_chiral_restr0.0661776
ELECTRON MICROSCOPYf_plane_restr0.0082009

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