[English] 日本語
Yorodumi
- EMDB-31959: Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31959
TitleHuman N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to ziconotide
Map data
Sample
  • Complex: CaV2.2-alpha2delta1-beta1 complex
    • Protein or peptide: Voltage-dependent N-type calcium channel subunit alpha-1B
    • Protein or peptide: Omega-conotoxin MVIIA
    • Protein or peptide: Voltage-dependent L-type calcium channel subunit beta-1
    • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1
  • Ligand: HEXADECANE
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / positive regulation of high voltage-gated calcium channel activity / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / membrane depolarization during bundle of His cell action potential / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / host cell presynaptic membrane ...regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / positive regulation of high voltage-gated calcium channel activity / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / membrane depolarization during bundle of His cell action potential / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / host cell presynaptic membrane / cardiac muscle cell action potential involved in contraction / NCAM1 interactions / regulation of ventricular cardiac muscle cell membrane repolarization / calcium ion transport into cytosol / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / ion channel inhibitor activity / neuromuscular junction development / calcium ion import across plasma membrane / Phase 0 - rapid depolarisation / neuronal dense core vesicle / regulation of heart rate by cardiac conduction / response to amyloid-beta / regulation of calcium ion transport / calcium channel regulator activity / voltage-gated calcium channel activity / T-tubule / sarcoplasmic reticulum / calcium ion transmembrane transport / modulation of chemical synaptic transmission / cellular response to amyloid-beta / calcium ion transport / amyloid-beta binding / toxin activity / chemical synaptic transmission / neuronal cell body / calcium ion binding / synapse / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, N-type, alpha-1 subunit / Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Voltage-dependent calcium channel, L-type, beta-1 subunit / Conotoxin / Conotoxin / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / VWA N-terminal ...Voltage-dependent calcium channel, N-type, alpha-1 subunit / Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Voltage-dependent calcium channel, L-type, beta-1 subunit / Conotoxin / Conotoxin / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / VWA N-terminal / Voltage-dependent calcium channel, alpha-2/delta subunit, conserved region / : / VWA N-terminal / Neuronal voltage-dependent calcium channel alpha 2acd / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / : / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Voltage-dependent channel domain superfamily / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / Ion transport domain / Ion transport protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Omega-conotoxin MVIIA / Voltage-dependent calcium channel subunit alpha-2/delta-1 / Voltage-dependent N-type calcium channel subunit alpha-1B / Voltage-dependent L-type calcium channel subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Conus magus (magus cone)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDong Y / Gao Y / Wang Y / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
CitationJournal: Cell Rep / Year: 2021
Title: Closed-state inactivation and pore-blocker modulation mechanisms of human Ca2.2.
Authors: Yanli Dong / Yiwei Gao / Shuai Xu / Yuhang Wang / Zhuoya Yu / Yue Li / Bin Li / Tian Yuan / Bei Yang / Xuejun Cai Zhang / Daohua Jiang / Zhuo Huang / Yan Zhao /
Abstract: N-type voltage-gated calcium (Ca) channels mediate Ca influx at presynaptic terminals in response to action potentials and play vital roles in synaptogenesis, release of neurotransmitters, and ...N-type voltage-gated calcium (Ca) channels mediate Ca influx at presynaptic terminals in response to action potentials and play vital roles in synaptogenesis, release of neurotransmitters, and nociceptive transmission. Here, we elucidate a cryo-electron microscopy (cryo-EM) structure of the human Ca2.2 complex in apo, ziconotide-bound, and two Ca2.2-specific pore blockers-bound states. The second voltage-sensing domain (VSD) is captured in a resting-state conformation, trapped by a phosphatidylinositol 4,5-bisphosphate (PIP) molecule, which is distinct from the other three VSDs of Ca2.2, as well as activated VSDs observed in previous structures of Ca channels. This structure reveals the molecular basis for the unique inactivation process of Ca2.2 channels, in which the intracellular gate formed by S6 helices is closed and a W-helix from the domain II-III linker stabilizes closed-state inactivation. The structures of this inactivated, drug-bound complex lay a solid foundation for developing new state-dependent blockers for treatment of chronic pain.
History
DepositionSep 13, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7vfu
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31959.png

Downloads & links

-
Map

FileDownload / File: emd_31959.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-3.1873765 - 5.2267923
Average (Standard dev.)0.0009372756 (±0.104250476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-3.1875.2270.001

-
Supplemental data

-
Sample components

+
Entire : CaV2.2-alpha2delta1-beta1 complex

EntireName: CaV2.2-alpha2delta1-beta1 complex
Components
  • Complex: CaV2.2-alpha2delta1-beta1 complex
    • Protein or peptide: Voltage-dependent N-type calcium channel subunit alpha-1B
    • Protein or peptide: Omega-conotoxin MVIIA
    • Protein or peptide: Voltage-dependent L-type calcium channel subunit beta-1
    • Protein or peptide: Voltage-dependent calcium channel subunit alpha-2/delta-1
  • Ligand: HEXADECANE
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: CaV2.2-alpha2delta1-beta1 complex

SupramoleculeName: CaV2.2-alpha2delta1-beta1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

+
Macromolecule #1: Voltage-dependent N-type calcium channel subunit alpha-1B

MacromoleculeName: Voltage-dependent N-type calcium channel subunit alpha-1B
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 262.831781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVRFGDELGG RYGGPGGGER ARGGGAGGAG GPGPGGLQPG QRVLYKQSIA QRARTMALYN PIPVKQNCFT VNRSLFVFSE DNVVRKYAK RITEWPPFEY MILATIIANC IVLALEQHLP DGDKTPMSER LDDTEPYFIG IFCFEAGIKI IALGFVFHKG S YLRNGWNV ...String:
MVRFGDELGG RYGGPGGGER ARGGGAGGAG GPGPGGLQPG QRVLYKQSIA QRARTMALYN PIPVKQNCFT VNRSLFVFSE DNVVRKYAK RITEWPPFEY MILATIIANC IVLALEQHLP DGDKTPMSER LDDTEPYFIG IFCFEAGIKI IALGFVFHKG S YLRNGWNV MDFVVVLTGI LATAGTDFDL RTLRAVRVLR PLKLVSGIPS LQVVLKSIMK AMVPLLQIGL LLFFAILMFA II GLEFYMG KFHKACFPNS TDAEPVGDFP CGKEAPARLC EGDTECREYW PGPNFGITNF DNILFAILTV FQCITMEGWT DIL YNTNDA AGNTWNWLYF IPLIIIGSFF MLNLVLGVLS GEFAKERERV ENRRAFLKLR RQQQIERELN GYLEWIFKAE EVML AEEDR NAEEKSPLDV LKRAATKKSR NDLIHAEEGE DRFADLCAVG SPFARASLKS GKTESSSYFR RKEKMFRFFI RRMVK AQSF YWVVLCVVAL NTLCVAMVHY NQPRRLTTTL YFAEFVFLGL FLTEMSLKMY GLGPRSYFRS SFNCFDFGVI VGSVFE VVW AAIKPGSSFG ISVLRALRLL RIFKVTKYWS SLRNLVVSLL NSMKSIISLL FLLFLFIVVF ALLGMQLFGG QFNFQDE TP TTNFDTFPAA ILTVFQILTG EDWNAVMYHG IESQGGVSKG MFSSFYFIVL TLFGNYTLLN VFLAIAVDNL ANAQELTK D EEEMEEAANQ KLALQKAKEV AEVSPMSAAN ISIAARQQNS AKARSVWEQR ASQLRLQNLR ASCEALYSEM DPEERLRFA TTRHLRPDMK THLDRPLVVE LGRDGARGPV GGKARPEAAE APEGVDPPRR HHRHRDKDKT PAAGDQDRAE APKAESGEPG AREERPRPH RSHSKEAAGP PEARSERGRG PGPEGGRRHH RRGSPEEAAE REPRRHRAHR HQDPSKECAG AKGERRARHR G GPRAGPRE AESGEEPARR HRARHKAQPA HEAVEKETTE KEATEKEAEI VEADKEKELR NHQPREPHCD LETSGTVTVG PM HTLPSTC LQKVEEQPED ADNQRNVTRM GSQPPDPNTI VHIPVMLTGP LGEATVVPSG NVDLESQAEG KKEVEADDVM RSG PRPIVP YSSMFCLSPT NLLRRFCHYI VTMRYFEVVI LVVIALSSIA LAAEDPVRTD SPRNNALKYL DYIFTGVFTF EMVI KMIDL GLLLHPGAYF RDLWNILDFI VVSGALVAFA FSGSKGKDIN TIKSLRVLRV LRPLKTIKRL PKLKAVFDCV VNSLK NVLN ILIVYMLFMF IFAVIAVQLF KGKFFYCTDE SKELERDCRG QYLDYEKEEV EAQPRQWKKY DFHYDNVLWA LLTLFT VST GEGWPMVLKH SVDATYEEQG PSPGYRMELS IFYVVYFVVF PFFFVNIFVA LIIITFQEQG DKVMSECSLE KNERACI DF AISAKPLTRY MPQNRQSFQY KTWTFVVSPP FEYFIMAMIA LNTVVLMMKF YDAPYEYELM LKCLNIVFTS MFSMECVL K IIAFGVLNYF RDAWNVFDFV TVLGSITDIL VTEIAETNNF INLSFLRLFR AARLIKLLRQ GYTIRILLWT FVQSFKALP YVCLLIAMLF FIYAIIGMQV FGNIALDDDT SINRHNNFRT FLQALMLLFR SATGEAWHEI MLSCLSNQAC DEQANATECG SDFAYFYFV SFIFLCSFLM LNLFVAVIMD NFEYLTRDSS ILGPHHLDEF IRVWAEYDPA ACGRISYNDM FEMLKHMSPP L GLGKKCPA RVAYKRLVRM NMPISNEDMT VHFTSTLMAL IRTALEIKLA PAGTKQHQCD AELRKEISVV WANLPQKTLD LL VPPHKPD EMTVGKVYAA LMIFDFYKQN KTTRDQMQQA PGGLSQMGPV SLFHPLKATL EQTQPAVLRG ARVFLRQKSS TSL SNGGAI QNQESGIKES VSWGTQRTQD APHEARPPLE RGHSTEIPVG RSGALAVDVQ MQSITRRGPD GEPQPGLESQ GRAA SMPRL AAETQPVTDA SPMKRSISTL AQRPRGTHLC STTPDRPPPS QASSHHHHHR CHRRRDRKQR SLEKGPSLSA DMDGA PSSA VGPGLPPGEG PTGCRRERER RQERGRSQER RQPSSSSSEK QRFYSCDRFG GREPPKPKPS LSSHPTSPTA GQEPGP HPQ GSGSVNGSPL LSTSGASTPG RGGRRQLPQT PLTPRPSITY KTANSSPIHF AGAQTSLPAF SPGRLSRGLS EHNALLQ RD PLSQPLAPGS RIGSDPYLGQ RLDSEASVHA LPEDTLTFEE AVATNSGRSS RTSYVSSLTS QSHPLRRVPN GYHCTLGL S SGGRARHSYH HPDQDHWC

+
Macromolecule #2: Omega-conotoxin MVIIA

MacromoleculeName: Omega-conotoxin MVIIA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Conus magus (magus cone)
Molecular weightTheoretical: 2.652216 KDa
SequenceString:
CKGKGAKCSR LMYDCCTGSC RSGKC

+
Macromolecule #3: Voltage-dependent L-type calcium channel subunit beta-1

MacromoleculeName: Voltage-dependent L-type calcium channel subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.799594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVQKTSMSRG PYPPSQEIPM EVFDPSPQGK YSKRKGRFKR SDGSTSSDTT SNSFVRQGSA ESYTSRPSDS DVSLEEDREA LRKEAERQA LAQLEKAKTK PVAFAVRTNV GYNPSPGDEV PVQGVAITFE PKDFLHIKEK YNNDWWIGRL VKEGCEVGFI P SPVKLDSL ...String:
MVQKTSMSRG PYPPSQEIPM EVFDPSPQGK YSKRKGRFKR SDGSTSSDTT SNSFVRQGSA ESYTSRPSDS DVSLEEDREA LRKEAERQA LAQLEKAKTK PVAFAVRTNV GYNPSPGDEV PVQGVAITFE PKDFLHIKEK YNNDWWIGRL VKEGCEVGFI P SPVKLDSL RLLQEQKLRQ NRLGSSKSGD NSSSSLGDVV TGTRRPTPPA SAKQKQKSTE HVPPYDVVPS MRPIILVGPS LK GYEVTDM MQKALFDFLK HRFDGRISIT RVTADISLAK RSVLNNPSKH IIIERSNTRS SLAEVQSEIE RIFELARTLQ LVA LDADTI NHPAQLSKTS LAPIIVYIKI TSPKVLQRLI KSRGKSQSKH LNVQIAASEK LAQCPPEMFD IILDENQLED ACEH LAEYL EAYWKATHPP SSTPPNPLLN RTMATAALAA SPAPVSNLQG PYLASGDQPL ERATGEHASM HEYPGELGQP PGLYP SSHP PGRAGTLRAL SRQDTFDADT PGSRNSAYTE LGDSCVDMET DPSEGPGLGD PAGGGTPPAR QGSWEDEEED YEEELT DNR NRGRNKARYC AEGGGPVLGR NKNELEGWGR GVYIR

+
Macromolecule #4: Voltage-dependent calcium channel subunit alpha-2/delta-1

MacromoleculeName: Voltage-dependent calcium channel subunit alpha-2/delta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 124.692469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGCLLALT LTLFQSLLIG PSSEEPFPSA VTIKSWVDKM QEDLVTLAKT ASGVNQLVDI YEKYQDLYTV EPNNARQLVE IAARDIEKL LSNRSKALVR LALEAEKVQA AHQWREDFAS NEVVYYNAKD DLDPEKNDSE PGSQRIKPVF IEDANFGRQI S YQHAAVHI ...String:
MAAGCLLALT LTLFQSLLIG PSSEEPFPSA VTIKSWVDKM QEDLVTLAKT ASGVNQLVDI YEKYQDLYTV EPNNARQLVE IAARDIEKL LSNRSKALVR LALEAEKVQA AHQWREDFAS NEVVYYNAKD DLDPEKNDSE PGSQRIKPVF IEDANFGRQI S YQHAAVHI PTDIYEGSTI VLNELNWTSA LDEVFKKNRE EDPSLLWQVF GSATGLARYY PASPWVDNSR TPNKIDLYDV RR RPWYIQG AASPKDMLIL VDVSGSVSGL TLKLIRTSVS EMLETLSDDD FVNVASFNSN AQDVSCFQHL VQANVRNKKV LKD AVNNIT AKGITDYKKG FSFAFEQLLN YNVSRANCNK IIMLFTDGGE ERAQEIFNKY NKDKKVRVFT FSVGQHNYDR GPIQ WMACE NKGYYYEIPS IGAIRINTQE YLDVLGRPMV LAGDKAKQVQ WTNVYLDALE LGLVITGTLP VFNITGQFEN KTNLK NQLI LGVMGVDVSL EDIKRLTPRF TLCPNGYYFA IDPNGYVLLH PNLQPKPIGV GIPTINLRKR RPNIQNPKSQ EPVTLD FLD AELENDIKVE IRNKMIDGES GEKTFRTLVK SQDERYIDKG NRTYTWTPVN GTDYSLALVL PTYSFYYIKA KLEETIT QA RYSETLKPDN FEESGYTFIA PRDYCNDLKI SDNNTEFLLN FNEFIDRKTP NNPSCNADLI NRVLLDAGFT NELVQNYW S KQKNIKGVKA RFVVTDGGIT RVYPKEAGEN WQENPETYED SFYKRSLDND NYVFTAPYFN KSGPGAYESG IMVSKAVEI YIQGKLLKPA VVGIKIDVNS WIENFTKTSI RDPCAGPVCD CKRNSDVMDC VILDDGGFLL MANHDDYTNQ IGRFFGEIDP SLMRHLVNI SVYAFNKSYD YQSVCEPGAA PKQGAGHRSA YVPSVADILQ IGWWATAAAW SILQQFLLSL TFPRLLEAVE M EDDDFTAS LSKQSCITEQ TQYFFDNDSK SFSGVLDCGN CSRIFHGEKL MNTNLIFIMV ESKGTCPCDT RLLIQAEQTS DG PNPCDMV KQPRYRKGPD VCFDNNVLED YTDCGGVSGL NPSLWYIIGI QFLLLWLVSG STHRLL

+
Macromolecule #7: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 7 / Number of copies: 18 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

+
Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

+
Macromolecule #9: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
type: ligand / ID: 9 / Number of copies: 1 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

+
Macromolecule #10: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 9.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5gjw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 203629
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more