[English] 日本語
Yorodumi
- PDB-8utp: KIF1A[1-393] - AMP-PNP two-heads-bound state in complex with a mi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8utp
TitleKIF1A[1-393] - AMP-PNP two-heads-bound state in complex with a microtubule - class T3L1
Components
  • Kinesin-like protein KIF1A
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / KIF1A / kinesin / motility / microtubule / tubulin
Function / homology
Function and homology information


neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / neuronal dense core vesicle / cytoskeletal motor activity / vesicle-mediated transport / axon cytoplasm / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / axon / GTPase activity / synapse / dendrite / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / PH domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin beta chain / Kinesin-like protein KIF1A / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBenoit, M.P.M.H. / Rao, L. / Asenjo, A.B. / Gennerich, A. / Sosa, H.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM113164 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098469 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01NS114636 United States
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD019994 United States
CitationJournal: To Be Published
Title: Cryo-EM of human KIF1A reveals its mechanism of motility and the effect of its pathogenic variant P305L
Authors: Benoit, M.P.M.H. / Rao, L. / Asenjo, A.B. / Gennerich, A. / Sosa, H.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
K: Kinesin-like protein KIF1A
N: Kinesin-like protein KIF1A
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
E: Tubulin alpha-1B chain
I: Tubulin beta-2B chain
S: Tubulin alpha-1B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,46320
Polymers349,1907
Non-polymers5,27313
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 3 types, 7 molecules KNAESBI

#1: Protein Kinesin-like protein KIF1A / Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A- ...Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A-related protein / hUnc-104


Mass: 49288.438 Da / Num. of mol.: 2 / Fragment: residues 1-393
Source method: isolated from a genetically manipulated source
Details: "linker" residues are comprised of a leucine zipper based on S. cerevisiae GCN4, which is followed by the C-terminal strep-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF1A, ATSV, C2orf20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12756
#2: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#3: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7

-
Non-polymers , 5 types, 13 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: KIF1A - AMP-PNP two-heads-bound state in complex with a microtubule - class T3LS
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 6.8
Buffer component
IDConc.NameBuffer-ID
180 mMK-PIPES1
220 uMPaclitaxel1
35 mMMagnesium chloride1
41 mMEGTA1
54 mMAMP-PNP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.22 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11168.095.6C1
21168.095.6C1
31168.095.6C1
41168.095.6C1
51168.095.6C1
61168.095.6C1
71168.095.6C1
81168.095.6C1
91168.095.6C1
101168.095.6C1
111168.095.6C1
121168.095.6C1
131168.095.6C1
141168.095.6C1
151168.095.6C1
161168.095.6C1
171168.095.6C1
181168.095.6C1
191168.095.6C1
201168.095.6C1
211168.095.6C1
221168.095.6C1
231168.095.6C1
241168.095.6C1
251168.095.6C1
261168.095.6C1
271168.095.6C1
281168.095.6C1
291168.095.6C1
301168.095.6C1
311168.095.6C1
321168.095.6C1
331168.095.6C1
341168.095.6C1
351168.095.6C1
361168.095.6C1
371168.095.6C1
381168.095.6C1
391168.095.6C1
401168.095.6C1
411168.095.6C1
421168.095.6C1
431168.095.6C1
441168.095.6C1
451168.095.6C1
461168.095.6C1
471168.095.6C1
481168.095.6C1
491168.095.6C1
501168.095.6C1
511168.095.6C1
521168.095.6C1
531168.095.6C1
541168.095.6C1
551168.095.6C1
561168.095.6C1
571168.095.6C1
581168.095.6C1
591168.095.6C1
601168.095.6C1
611168.095.6C1
621168.095.6C1
631168.095.6C1
641168.095.6C1
652168.095.6C1
662168.095.6C1
672168.095.6C1
682168.095.6C1
692168.095.6C1
702168.095.6C1
712168.095.6C1
722168.095.6C1
732168.095.6C1
742168.095.6C1
752168.095.6C1
762168.095.6C1
772168.095.6C1
782168.095.6C1
792168.095.6C1
802168.095.6C1
812168.095.6C1
822168.095.6C1
832168.095.6C1
842168.095.6C1
852168.095.6C1
862168.095.6C1
872168.095.6C1
882168.095.6C1
892168.095.6C1
902168.095.6C1
912168.095.6C1
922168.095.6C1
932168.095.6C1
942168.095.6C1
952168.095.6C1
962168.095.6C1
972168.095.6C1
982168.095.6C1
992168.095.6C1
1002168.095.6C1
1012168.095.6C1
1022168.095.6C1
1032168.095.6C1
1042168.095.6C1
1052168.095.6C1
1062168.095.6C1
1072168.095.6C1
1082168.095.6C1
1092168.095.6C1
1102168.095.6C1
1112168.095.6C1
1122168.095.6C1
1132168.095.6C1
1142168.095.6C1
1152168.095.6C1
1162168.095.6C1
1172168.095.6C1
1182168.095.6C1
1192168.095.6C1
1202168.095.6C1
1212168.095.6C1
1222168.095.6C1
1232168.095.6C1
1242168.095.6C1
1252168.095.6C1
1262168.095.6C1
1272168.095.6C1
1282168.095.6C1
3D reconstruction

Entry-ID: 8UTP / Num. of particles: 89711 / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: HELICAL

IDResolution (Å)Image processing-IDDetails
13.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
23.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED
33.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
43.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
53.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
63.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED
73.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
83.21NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
93.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
103.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED
113.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
123.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
133.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
143.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED
153.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
163.22NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED.
RefinementHighest resolution: 3.2 Å

+
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://pdbjlvh1.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