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- EMDB-65778: Cryo-EM structure of the kinesin-2 tail domain in complex with KA... -

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Basic information

Entry
Database: EMDB / ID: EMD-65778
TitleCryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC
Map datasharpened map
Sample
  • Complex: Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC
    • Protein or peptide: Kinesin-like protein KIF3A
    • Protein or peptide: Kinesin-like protein KIF3B, N-terminally processed
    • Protein or peptide: Kinesin-associated protein 3
    • Protein or peptide: Adenomatous polyposis coli protein
KeywordsKinesin-2 motor Intracellular transport Kinesin-adaptor-cargo complex / MOTOR PROTEIN
Function / homology
Function and homology information


negative regulation of odontogenesis / axis specification / positive regulation of calcium-dependent cell-cell adhesion / kinesin II complex / opsin transport / negative regulation of epithelial cell proliferation involved in prostate gland development / intraciliary transport particle B binding / isoflavonoid biosynthetic process / Apoptotic cleavage of cellular proteins / periciliary membrane compartment ...negative regulation of odontogenesis / axis specification / positive regulation of calcium-dependent cell-cell adhesion / kinesin II complex / opsin transport / negative regulation of epithelial cell proliferation involved in prostate gland development / intraciliary transport particle B binding / isoflavonoid biosynthetic process / Apoptotic cleavage of cellular proteins / periciliary membrane compartment / Beta-catenin phosphorylation cascade / Intraflagellar transport / proximal/distal pattern formation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nitrogen cycle metabolic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of epithelial cell differentiation / Deactivation of the beta-catenin transactivating complex / intraciliary transport / Ovarian tumor domain proteases / anterograde dendritic transport of neurotransmitter receptor complex / Kinesins / negative regulation of cell cycle G1/S phase transition / Scrib-APC-beta-catenin complex / : / COPI-dependent Golgi-to-ER retrograde traffic / photoreceptor connecting cilium / Degradation of beta-catenin by the destruction complex / gamma-catenin binding / negative regulation of cardiac muscle cell proliferation / regulation of attachment of spindle microtubules to kinetochore / cell body fiber / cilium organization / metaphase/anaphase transition of mitotic cell cycle / pattern specification process / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / cell projection membrane / negative regulation of microtubule depolymerization / regulation of osteoclast differentiation / anterior/posterior pattern specification / MHC class II antigen presentation / S-adenosylmethionine-dependent methyltransferase activity / beta-catenin destruction complex / dorsal/ventral pattern formation / catenin complex / microtubule plus-end binding / protein kinase regulator activity / cell fate specification / O-methyltransferase activity / muscle cell cellular homeostasis / regulation of microtubule-based process / protein-containing complex localization / skin development / microtubule motor activity / kinesin complex / negative regulation of G1/S transition of mitotic cell cycle / somatic stem cell population maintenance / stem cell population maintenance / microtubule-based movement / mitotic spindle assembly checkpoint signaling / regulation of osteoblast differentiation / hair follicle development / positive regulation of cytokinesis / ciliary transition zone / neuron projection terminus / canonical Wnt signaling pathway / regulation of cell differentiation / establishment or maintenance of cell polarity / negative regulation of Wnt signaling pathway / mitotic cytokinesis / positive regulation of cell division / dynein complex binding / lateral plasma membrane / mitotic spindle assembly / chromosome organization / bicellular tight junction / cilium assembly / photoreceptor outer segment / axoneme / kinesin binding / axonal growth cone / retina development in camera-type eye / microtubule-based process / thymus development / positive regulation of microtubule polymerization / negative regulation of MAPK cascade / axonogenesis / vesicle-mediated transport / cell projection / cytoplasmic microtubule organization / kidney development / photoreceptor inner segment / regulation of cell migration / positive regulation of cell adhesion / dendrite cytoplasm / condensed nuclear chromosome / spindle microtubule / adherens junction / positive regulation of cell differentiation
Similarity search - Function
Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein ...Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Kinesin-like protein / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Armadillo/beta-catenin-like repeats / Armadillo / Kinesin motor domain superfamily / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Coniferyl alcohol 9-O-methyltransferase / Kinesin-associated protein 3 / Adenomatous polyposis coli protein / Kinesin-like protein KIF3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJiang X / Danev R / Yanagisawa H / Kikkawa M
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER2202 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05247 Japan
Japan Society for the Promotion of Science (JSPS)JP24KF0141 Japan
Japan Society for the Promotion of Science (JSPS)JP24K18106 Japan
CitationJournal: Sci Adv / Year: 2025
Title: The hook-like adaptor and cargo-binding (HAC) domain in the kinesin-2 tail enables adaptor assembly and cargo recognition.
Authors: Xuguang Jiang / Radostin Danev / Sotaro Ichinose / Baichun Niu / Sumio Ohtsuki / Haruaki Yanagisawa / Satoru Nagatoishi / Kouhei Tsumoto / Nobutaka Hirokawa / Masahide Kikkawa /
Abstract: Intracellular transport relies on motor proteins such as kinesins to deliver cargo along microtubules, yet how they recognize cargo remains unclear. Here, we present high-resolution cryo-electron ...Intracellular transport relies on motor proteins such as kinesins to deliver cargo along microtubules, yet how they recognize cargo remains unclear. Here, we present high-resolution cryo-electron microscopy structures of the heterotrimeric kinesin-2 complex (KIF3A/KIF3B/KAP3) bound to the cargo protein APC. Our findings reveal a previously uncharacterized KIF3 tail hook-like motif, termed the "HAC" domain, which mediates binding to both KAP3 adaptor and APC cargo. Within this domain, the KIF3A helical regions ensure cargo specificity, while a β-hairpin and KIF3B provide structural support. Biochemical and neuronal experiments confirm its functional importance. Notably, the HAC/KAP3 structure resembles hook-like architectures seen in kinesin-1 and dynein, suggesting a shared cargo recognition framework. These findings also shed light on kinesin-2 cargo specificity and offer a structural framework for understanding related neuronal transport mechanisms.
History
DepositionAug 10, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65778.png

Downloads & links

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Map

FileDownload / File: emd_65778.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 160 pix.
= 208. Å		1.3 Å/pix.
x 160 pix.
= 208. Å		1.3 Å/pix.
x 160 pix.
= 208. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.0017263165 - 2.4871056
Average (Standard dev.)0.0019050711 (±0.029757828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map

Fileemd_65778_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: halfmap2

Fileemd_65778_half_map_1.map
Annotationhalfmap2
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_65778_half_map_2.map
Annotationhalfmap1
Projections & Slices
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Sample components

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Entire : Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC

EntireName: Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC
Components
  • Complex: Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC
    • Protein or peptide: Kinesin-like protein KIF3A
    • Protein or peptide: Kinesin-like protein KIF3B, N-terminally processed
    • Protein or peptide: Kinesin-associated protein 3
    • Protein or peptide: Adenomatous polyposis coli protein

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Supramolecule #1: Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC

SupramoleculeName: Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Kinesin-like protein KIF3A

MacromoleculeName: Kinesin-like protein KIF3A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.084143 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SQSLQEEAQG KTKKLKKVWT MLMAAKSEMA DLQQEHQREI EGLLENIRQL SRELRLQMLI IDNFIPQDYQ EMIENYVHW NEDIGEWQLK CVAYTGNNMR KQTPVPDKKE RDPFEVDLSH VYLAYTEESL RQSLMKLERP RTSKGKARPK M GRRKRSAK PETVIDSLLQ

UniProtKB: Coniferyl alcohol 9-O-methyltransferase

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Macromolecule #2: Kinesin-like protein KIF3B, N-terminally processed

MacromoleculeName: Kinesin-like protein KIF3B, N-terminally processed / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.440057 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLQQEVDIK TKKLKKLFSK LQAVKAEIHD LQEEHIKERQ ELEQTQNELT RELKLKHLII ENFIPLEEKN KIMNRSFFDD EEDHWKLHP ITRLENQQMM KRPVSAVGYK RPLSQHARMS MMIRPEPRYR AENIMLLELD MPSRTTRDYE GPAISPKVQA A LDAALQDE ...String:
MSLQQEVDIK TKKLKKLFSK LQAVKAEIHD LQEEHIKERQ ELEQTQNELT RELKLKHLII ENFIPLEEKN KIMNRSFFDD EEDHWKLHP ITRLENQQMM KRPVSAVGYK RPLSQHARMS MMIRPEPRYR AENIMLLELD MPSRTTRDYE GPAISPKVQA A LDAALQDE DEIQVDASSF ESTASRKPKA RPKSGRKSGS SSSSSGNPAS QFYPQSRGLV PK

UniProtKB: Kinesin-like protein KIF3B

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Macromolecule #3: Kinesin-associated protein 3

MacromoleculeName: Kinesin-associated protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 80.224148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQGEDARYLK RKVKGGNIDV HPSEKALIVQ YEVEATILGE MGDPMLGERK ECQKIIRLKS LNANTDITSL ARKVVEECKL IHPSKLSEV EQLLYYLQNR RDSLPGKEKK EKSSKPKDPP PFEGMEIDEV ANINDMDEYI ELLYEDIPDK VRGSALILQL A RNPDNLEE ...String:
MQGEDARYLK RKVKGGNIDV HPSEKALIVQ YEVEATILGE MGDPMLGERK ECQKIIRLKS LNANTDITSL ARKVVEECKL IHPSKLSEV EQLLYYLQNR RDSLPGKEKK EKSSKPKDPP PFEGMEIDEV ANINDMDEYI ELLYEDIPDK VRGSALILQL A RNPDNLEE LLLNETALGA LARVLREDWK QSVELATNII YIFFCFSSFS HFHGLITHYK IGALCMNIID HELKRHELWQ EE LSKKKKA VDEDLENQTL RKDYDKTFKK YQGLVVKQEQ LLRVALYLLL NLAEDTRTEL KMRNKNIVHM LVKALDRDNF ELL ILVVSF LKKLSIFMEN KNDMVEMDIV EKLVKMIPCE HEDLLNITLR LLLNLSFDTG LRNKMVQVGL LPKLTALLGN ENYK QIAMC VLYHISMDDR FKSMFAYTDC IPQLMKMLFE CSDERIDLEL ISFCINLAAN KRNVQLICEG NGLKMLMKRA LKLKD PLLM KMIRNISQHD GPTKNLFIDY VGDLAAQISS DEEEEFVIEC LGTLANLTIP DLDWELVLKE YKLVPFLKDK LKPGAA EDD LVLEVVIMIG TVSMDDSCAA LLAKSGIIPA LIELLNAQQE DDEFVCQIIY VFYQMVFHQA TRDVIIKETQ APAYLID LM HDKNNEIRKV CDNTLDIIAE YDEEWAKKIQ SEKFRWHNSQ WLEMVESRQL D

UniProtKB: Kinesin-associated protein 3

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Macromolecule #4: Adenomatous polyposis coli protein

MacromoleculeName: Adenomatous polyposis coli protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 75.417633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSQD SCISMRQSGC LPLLIQLLHG NDKDSVLLGN SRGSKEARAR ASAALHNIIH SQPDDKRGRR EIRVLHLLEQ IRAYCETCW EWQEAHEQGM DQDKNPMPAP VEHQICPAVC VLMKLSFDEE HRHAMNELGG LQAIAELLQV DCEMYGLTND H YSVTLRRY ...String:
MHHHHHHSQD SCISMRQSGC LPLLIQLLHG NDKDSVLLGN SRGSKEARAR ASAALHNIIH SQPDDKRGRR EIRVLHLLEQ IRAYCETCW EWQEAHEQGM DQDKNPMPAP VEHQICPAVC VLMKLSFDEE HRHAMNELGG LQAIAELLQV DCEMYGLTND H YSVTLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK AL MECALEV KKESTLKSVL SALWNLSAHC TENKADICAV DGALAFLVGT LTYRSQTNTL AIIESGGGIL RNVSSLIATN EDH RQILRE NNCLQTLLQH LKSHSLTIVS NACGTLWNLS ARNPKDQEAL WDMGAVSMLK NLIHSKHKMI AMGSAAALRN LMAN RPAKY KDANIMSPGS SLPSLHVRKQ KALEAELDAQ HLSETFDNID NLSPKASHRS KQRHKQNLYG DYAFDANRHD DSRSD NFNT GNMTVLSPYL NTTVLPSSSS SRGSLDSSRS EKDRSLERER GIGLSAYHPT TENAGTSSKR GLQITTTAAQ IAKVME EVS AIHTSQDDRS SASTTEFHCV ADDRSAARRS SASHTHSNTY NFTKSENSNR TCSMPYAKVE YKRSSNDSLN SVTSSDG YG KRGQMKPSVE SYSEDDESKF CSYGQYPADL AHKIHSAN

UniProtKB: Adenomatous polyposis coli protein

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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

Concentration0.0375 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 36020 / Average electron dose: 64.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.55 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 80000
Sample stageCooling holder cryogen: NITROGEN

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 19918 / Average electron dose: 63.0 e/Å2
Details: tilted-stage image collection with tilt angles of 30 and 40 degrees
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 12833027
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 407310
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

9w9h

source_name: PDB, initial_model_type: experimental modelchains, A-C

4yje

source_name: PDB, initial_model_type: experimental modelchain D
DetailsInitial local fitting was done using Phenix dock-in-map tool.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9w9i:
Cryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC

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