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- EMDB-20217: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin ad... -

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Basic information

Entry
Database: EMDB / ID: EMD-20217
TitleStructure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
Map data
Sample
  • Complex: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
    • Protein or peptide: AP-2 complex subunit alpha
    • Protein or peptide: AP-2 complex subunit beta
    • Protein or peptide: Adaptor protein complex AP-2, mu1Adapter
    • Protein or peptide: Tetherin,Protein Nef
    • Protein or peptide: AP-2 complex subunit sigma
Function / homology
Function and homology information


AP-type membrane coat adaptor complex / Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / Retrograde neurotrophin signalling ...AP-type membrane coat adaptor complex / Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / clathrin coat / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / VLDLR internalisation and degradation / cardiac septum development / virus-mediated perturbation of host defense response => GO:0019049 / MHC class II antigen presentation / Recycling pathway of L1 / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / vesicle budding from membrane / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / neurotransmitter receptor internalization / positive regulation of protein localization to membrane / coronary vasculature development / signal sequence binding / negative regulation of protein localization to plasma membrane / aorta development / Neutrophil degranulation / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / protein serine/threonine kinase binding / positive regulation of endocytosis / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / vesicle-mediated transport / phosphatidylinositol binding / secretory granule / kidney development / intracellular protein transport / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / synaptic vesicle / presynapse / heart development / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / defense response to virus / transmembrane transporter binding / membrane => GO:0016020 / protein domain specific binding / intracellular membrane-bounded organelle / glutamatergic synapse / lipid binding / synapse / protein-containing complex binding / GTP binding / protein kinase binding / mitochondrion / plasma membrane
Similarity search - Function
Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain ...Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Tetherin variant Sm2 / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / Protein Nef / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse) / Simian immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBuffalo CZ / Ren X / Hurley JH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 GM125209 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120691 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission.
Authors: Cosmo Z Buffalo / Christina M Stürzel / Elena Heusinger / Dorota Kmiec / Frank Kirchhoff / James H Hurley / Xuefeng Ren /
Abstract: Tetherin is a host defense factor that physically prevents virion release from the plasma membrane. The Nef accessory protein of simian immunodeficiency virus (SIV) engages the clathrin adaptor AP-2 ...Tetherin is a host defense factor that physically prevents virion release from the plasma membrane. The Nef accessory protein of simian immunodeficiency virus (SIV) engages the clathrin adaptor AP-2 to downregulate tetherin via its DIWK motif. As human tetherin lacks DIWK, antagonism of tetherin by Nef is a barrier to simian-human transmission of non-human primate lentiviruses. To determine the molecular basis for tetherin counteraction, we reconstituted the AP-2 complex with a simian tetherin and SIV Nef and determined its structure by cryoelectron microscopy (cryo-EM). Nef refolds the first α-helix of the β2 subunit of AP-2 to a β hairpin, creating a binding site for the DIWK sequence. The tetherin binding site in Nef is distinct from those of most other Nef substrates, including MHC class I, CD3, and CD4 but overlaps with the site for the restriction factor SERINC5. This structure explains the dependence of SIVs on tetherin DIWK and consequent barrier to human transmission.
History
DepositionMay 10, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseSep 25, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.485
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.485
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6owt
  • Surface level: 0.485
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20217.png

Downloads & links

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Map

FileDownload / File: emd_20217.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.149 Å
Density
Contour LevelBy AUTHOR: 0.485 / Movie #1: 0.485
Minimum - Maximum-2.185999 - 3.475225
Average (Standard dev.)0.0033728944 (±0.06059342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1491.1491.149
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.144294.144294.144
α/β/γ90.00090.00090.000
start NX/NY/NZ1548552
NX/NY/NZ198170217
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.1863.4750.003

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Supplemental data

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Sample components

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Entire : Structure of SIVsmm Nef and SMM tetherin bound to the clathrin ad...

EntireName: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
Components
  • Complex: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
    • Protein or peptide: AP-2 complex subunit alpha
    • Protein or peptide: AP-2 complex subunit beta
    • Protein or peptide: Adaptor protein complex AP-2, mu1Adapter
    • Protein or peptide: Tetherin,Protein Nef
    • Protein or peptide: AP-2 complex subunit sigma

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Supramolecule #1: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin ad...

SupramoleculeName: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 203.6 KDa

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Macromolecule #1: AP-2 complex subunit alpha

MacromoleculeName: AP-2 complex subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 104.286391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAVSKGEGM RGLAVFISDI RNCKSKEAEI KRINKELANI RSKFKGDKAL DGYSKKKYVC KLLFIFLLGH DIDFGHMEAV NLLSSNRYT EKQIGYLFIS VLVNSNSELI RLINNAIKND LASRNPTFMG LALHCIANVG SREMAEAFAG EIPKILVAGD T MDSVKQSA ...String:
MPAVSKGEGM RGLAVFISDI RNCKSKEAEI KRINKELANI RSKFKGDKAL DGYSKKKYVC KLLFIFLLGH DIDFGHMEAV NLLSSNRYT EKQIGYLFIS VLVNSNSELI RLINNAIKND LASRNPTFMG LALHCIANVG SREMAEAFAG EIPKILVAGD T MDSVKQSA ALCLLRLYRT SPDLVPMGDW TSRVVHLLND QHLGVVTAAT SLITTLAQKN PEEFKTSVSL AVSRLSRIVT SA STDLQDY TYYFVPAPWL SVKLLRLLQC YPPPEDPAVR GRLTECLETI LNKAQEPPKS KKVQHSNAKN AVLFEAISLI IHH DSEPNL LVRACNQLGQ FLQHRETNLR YLALESMCTL ASSEFSHEAV KTHIETVINA LKTERDVSVR QRAVDLLYAM CDRS NAQQI VAEMLSYLET ADYSIREEIV LKVAILAEKY AVDYTWYVDT ILNLIRIAGD YVSEEVWYRV IQIVINRDDV QGYAA KTVF EALQAPACHE NLVKVGGYIL GEFGNLIAGD PRSSPLIQFN LLHSKFHLCS VPTRALLLST YIKFVNLFPE VKATIQ DVL RSDSQLKNAD VELQQRAVEY LRLSTVASTD ILATVLEEMP PFPERESSIL AKLKKKKGPS TVTDLEETKR ERSIDVN GG PEPVPASTSA ASTPSPSADL LGLGAVPPAP TGPPPTSGGG LLVDVFSDSA SAVAPLAPGS EDNFARFVCK NNGVLFEN Q LLQIGLKSEF RQNLGRMFIF YGNKTSTQFL NFTPTLICAD DLQTNLNLQT KPVDPTVDGG AQVQQVVNIE CISDFTEAP VLNIQFRYGG TFQNVSVKLP ITLNKFFQPT EMASQDFFQR WKQLSNPQQE VQNIFKAKHP MDTEITKAKI IGFGSALLEE VDPNPANFV GAGIIHTKTT QIGCLLRLEP NLQAQMYRLT LRTSKDTVSQ RLCELLSEQF

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Macromolecule #2: AP-2 complex subunit beta

MacromoleculeName: AP-2 complex subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 66.953195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDSKYFTTN KKGEIFELKA ELNNEKKEKR KEAVKKVIAA MTVGKDVSSL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN SFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQMVEDQ G FLDSLRDL ...String:
MTDSKYFTTN KKGEIFELKA ELNNEKKEKR KEAVKKVIAA MTVGKDVSSL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN SFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQMVEDQ G FLDSLRDL IADSNPMVVA NAVAALSEIS ESHPNSNLLD LNPQNINKLL TALNECTEWG QIFILDCLSN YNPKDDREAQ SI CERVTPR LSHANSAVVL SAVKVLMKFL ELLPKDSDYY NMLLKKLAPP LVTLLSGEPE VQYVALRNIN LIVQKRPEIL KQE IKVFFV KYNDPIYVKL EKLDIMIRLA SQANIAQVLA ELKEYATEVD VDFVRKAVRA IGRCAIKVEQ SAERCVSTLL DLIQ TKVNY VVQEAIVVIR DIFRKYPNKY ESIIATLCEN LDSLDEPDAR AAMIWIVGEY AERIDNADEL LESFLEGFHD ESTQV QLTL LTAIVKLFLK KPSETQELVQ QVLSLATQDS DNPDLRDRGY IYWRLLSTDP VTAKEVVLSE KPLISEETDL IEPTLL DEL ICHIGSLASV YHKPPNAFVE GSHGIHRK

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Macromolecule #3: Adaptor protein complex AP-2, mu1

MacromoleculeName: Adaptor protein complex AP-2, mu1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.161563 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIGGLFIYNH KGEVLISRVY RDDIGRNAVD AFRVNVIHAR QQVRSPVTNI ARTSFFHVKR SNIWLAAVTK QNVNAAMVFE FLYKMCDVM AAYFGKISEE NIKNNFVLIY ELLDEILDFG YPQNSETGAL KTFITQQGIK SQ

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Macromolecule #4: Tetherin,Protein Nef

MacromoleculeName: Tetherin,Protein Nef / type: protein_or_peptide / ID: 4
Details: protein chimera of the cytoplasmic tail of sooty mangabey (smm) linked to the N-terminus of SIV smm tetherin
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 31.772352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ILYDYSRMPM GDIWKEDGDK RSKGSDEASE GSGMGGVTSK KQSKRRQGLR ERLLQARGET DGYSRSRGEL GKGWNLPSAE GQGYSEEQF MNTPWRNPAR EGEKLKYRQQ NMDDVDDDDD ELVGVAVHPK VPLRAMSYKL AIDMSHFIKE KGGLEGIYYS D RRHRILDI ...String:
ILYDYSRMPM GDIWKEDGDK RSKGSDEASE GSGMGGVTSK KQSKRRQGLR ERLLQARGET DGYSRSRGEL GKGWNLPSAE GQGYSEEQF MNTPWRNPAR EGEKLKYRQQ NMDDVDDDDD ELVGVAVHPK VPLRAMSYKL AIDMSHFIKE KGGLEGIYYS D RRHRILDI YLEKEEGIIP DWQNYTSGPG VRYPLFFGWL WKLVPVNVSD EAQEDETHCL VHPAQTSQWD DPWGEVLAWK FD PKLAYTY EAFIRYPEEF GNDSGLSKEE VKRRLTAR

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Macromolecule #5: AP-2 complex subunit sigma

MacromoleculeName: AP-2 complex subunit sigma / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 17.011662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIRFILIQNR AGKTRLAKWY MQFDDDEKQK LIEEVHAVVT VRDAKHTNFV EFRNFKIIYR RYAGLYFCIC VDVNDNNLAY LEAIHNFVE VLNEYFHCVS ELDLVFNFYK VYTVVDEMFL AGEIRETSQT KVLKQLLMLQ SLE

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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

Concentration0.7 mg/mL
BufferpH: 8
GridModel: C-flat-2/1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa / Details: 25mA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.16 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159406
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

4nee

,

2xa7

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Output model

PDB-6owt:
Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex

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