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- EMDB-6992: Structure of the human PKD1/PKD2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6992
TitleStructure of the human PKD1/PKD2 complex
Map data
Sample
  • Complex: the structure of human PKD1/PKD2 complex
    • Protein or peptide: human PKD2 (chain F,G)
    • Protein or peptide: human PKD1 (chain B)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSu Q / Hu F / Ge X / Lei J / Yu S / Wang T / Zhou Q / Mei C / Shi Y
CitationJournal: Science / Year: 2018
Title: Structure of the human PKD1-PKD2 complex.
Authors: Qiang Su / Feizhuo Hu / Xiaofei Ge / Jianlin Lei / Shengqiang Yu / Tingliang Wang / Qiang Zhou / Changlin Mei / Yigong Shi /
Abstract: Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron ...Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron microscopy structure of truncated human PKD1-PKD2 complex assembled in a 1:3 ratio. PKD1 contains a voltage-gated ion channel (VGIC) fold that interacts with PKD2 to form the domain-swapped, yet noncanonical, transient receptor potential (TRP) channel architecture. The S6 helix in PKD1 is broken in the middle, with the extracellular half, S6a, resembling pore helix 1 in a typical TRP channel. Three positively charged, cavity-facing residues on S6b may block cation permeation. In addition to the VGIC, a five-transmembrane helix domain and a cytosolic PLAT domain were resolved in PKD1. The PKD1-PKD2 complex structure establishes a framework for dissecting the function and disease mechanisms of the PKD proteins.
History
DepositionJun 30, 2018-
Header (metadata) releaseAug 15, 2018-
Map releaseAug 15, 2018-
UpdateSep 19, 2018-
Current statusSep 19, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6992.png

Downloads & links

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Map

FileDownload / File: emd_6992.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.296 Å		1.09 Å/pix.
x 256 pix.
= 279.296 Å		1.09 Å/pix.
x 256 pix.
= 279.296 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.12242917 - 0.21744779
Average (Standard dev.)0.00071837305 (±0.0076906257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.296 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.296279.296279.296
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1220.2170.001

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Supplemental data

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Sample components

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Entire : the structure of human PKD1/PKD2 complex

EntireName: the structure of human PKD1/PKD2 complex
Components
  • Complex: the structure of human PKD1/PKD2 complex
    • Protein or peptide: human PKD2 (chain F,G)
    • Protein or peptide: human PKD1 (chain B)

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Supramolecule #1: the structure of human PKD1/PKD2 complex

SupramoleculeName: the structure of human PKD1/PKD2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Samples were obtained by co-expression in 293F cells. A complex contains one PKD1 subunit and three PKD2 subunits.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mammalian expression vector pCK9 (others) / Recombinant cell: 293F cells

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Macromolecule #1: human PKD2 (chain F,G)

MacromoleculeName: human PKD2 (chain F,G) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mammalian expression vector pCK9 (others)
SequenceString: PRVAWAERLV RGLRGLWGTR LMEESSTNRE KYLKSVLREL VTYLLFLIVL CILTYGMMSS NVYYYTRMMS QLFLDTPVSK TEKTNFKTL SSMEDFWKFT EGSLLDGLYW KMQPSNQTEA DNRSFIFYEN LLLGVPRIRQ LRVRNGSCSI PQDLRDEIKE C YDVYSVSS ...String:
PRVAWAERLV RGLRGLWGTR LMEESSTNRE KYLKSVLREL VTYLLFLIVL CILTYGMMSS NVYYYTRMMS QLFLDTPVSK TEKTNFKTL SSMEDFWKFT EGSLLDGLYW KMQPSNQTEA DNRSFIFYEN LLLGVPRIRQ LRVRNGSCSI PQDLRDEIKE C YDVYSVSS EDRAPFGPRN GTAWIYTSEK DLNGSSHWGI IATYSGAGYY LDLSRTREET AAQVASLKKN VWLDRGTRAT FI DFSVYNA NINLFCVVRL LVEFPATGGV IPSWQFQPLK LIRYVTTFDF FLAACEIIFC FFIFYYVVEE ILEIRIHKLH YFR SFWNCL DVVIVVLSVV AIGINIYRTS NVEVLLQFLE DQNTFPNFEH LAYWQIQFNN IAAVTVFFVW IKLFKFINFN RTMS QLSTT MSRCAKDLFG FAIMFFIIFL AYAQLAYLVF GTQVDDFSTF QECIFTQFRI ILGDINFAEI EEANRVLGPI YFTTF VFFM FFILLNMFLA IINDTYSEVK SDLAQQKAEM ELSDLIRKGY HKALVKLKLK KNTVD

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Macromolecule #2: human PKD1 (chain B)

MacromoleculeName: human PKD1 (chain B) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mammalian expression vector pCK9 (others)
SequenceString: TAFGASLFVP PSHVRFVFPE PTADVNYIVM LTCAVCLVTY MVMAAILHKL DQLDASRGRA IPFCGQRGRF KYEILVKTGW GRGSGTTAH VGIMLYGVDS RSGHRHLDGD RAFHRNSLDI FRIATPHSLG SVWKIRVWHD NKGLSPAWFL QHVIVRDLQT A RSAFFLVN ...String:
TAFGASLFVP PSHVRFVFPE PTADVNYIVM LTCAVCLVTY MVMAAILHKL DQLDASRGRA IPFCGQRGRF KYEILVKTGW GRGSGTTAH VGIMLYGVDS RSGHRHLDGD RAFHRNSLDI FRIATPHSLG SVWKIRVWHD NKGLSPAWFL QHVIVRDLQT A RSAFFLVN DWLSVETEAN GGLVEKEVLA ASDAALLRFR RLLVAELQRG FFDKHIWLSI WDRPPRSRFT RIQRATCCVL LI CLFLGAN AVWYGAVGDS AYSTGHVSRL SPLSVDTVAV GLVSSVVVYP VYLAILFLFR MSRSKVAGSP SPTPAGQQVL DID SCLDSS VLDSSFLTFS GLHAEQAFVG QMKSDLFLDD SKSLVCWPSG EGTLSWPDLL SDPSIVGSNL RQLARGQAGH GLGP EEDGF SLASPYSPAK SFSASDEDLI QQVLAEGVSS PAPTQDTHME TDLLSSLSST PGEKTETLAL QRLGELGPPS PGLNW EQPQ AARLSRTGLV EGLRKRLLPA WCASLAHGLS LLLVAVAVAV SGWVGASFPP GVSVAWLLSS SASFLASFLG WEPLKV LLE ALYFSLVAKR LHPDEDDTLV ESPAVTPVSA RVPRVRPPHG FALFLAKEEA RKVKRLHGML RSLLVYMLFL LVTLLAS YG DASCHGHAYR LQSAIKQELH SRAFLAITRS EELWPWMAHV LLPYVHGNQS SPELGPPRLR QVRLQEALYP DPPGPRVH T CSAAGGFSTS DYDVGWESPH NGSGTWAYSA PDLLGAWSWG SCAVYDSGGY VQELGLSLEE SRDRLRFLQL HNWLDNRSR AVFLELTRYS PAVGLHAAVT LRLEFPAAGR ALAALSVRPF ALRRLSAGLS LPLLTSVCLL LFAVHFAVAE ARTWHREGRW RVLRLGAWA RWLLVALTAA TALVRLAQLG AADRQWTRFV RGRPRRFTSF DQVAQLSSAA RGLAASLLFL LLVKAAQQLR F VRQWSVFG KTLCRALPEL LGVTLGLVVL GVAYAQLAIL LVSSCVDSLW SVAQALLVLC PGTGLSTLCP AESWHLSPLL CV GLWALRL WGALRLGAVI LRWRYHALRG ELYRPAWEPQ DYEMVELFLR RLRLWMGLSK VKEFRHKVRF EGMEPLPSRS SRG S

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPESHEPES 7.5
0.06 %digitonindigitonin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t4d

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116485
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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