[English] 日本語
Yorodumi
- PDB-1kil: Three-dimensional structure of the complexin/SNARE complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kil
TitleThree-dimensional structure of the complexin/SNARE complex
Components
  • Complexin I SNARE-complex binding region
  • SNAP-25 C-terminal SNARE motif
  • SNAP-25 N-terminal SNARE motif
  • Synaptobrevin SNARE motif
  • Syntaxin SNARE motif short
KeywordsMEMBRANE PROTEIN / Helix bound to four helix bundle
Function / homology
Function and homology information


regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling ...regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type A (botA) / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / zymogen granule membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / storage vacuole / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / eosinophil degranulation / vesicle fusion / vesicle docking / neurotransmitter transmembrane transporter activity / positive regulation of calcium ion-dependent exocytosis / regulation of neurotransmitter secretion / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / regulation of exocytosis / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / regulation of synaptic vesicle recycling / Sensory processing of sound by inner hair cells of the cochlea / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / Other interleukin signaling / myosin binding / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / calyx of Held / regulation of insulin secretion / positive regulation of excitatory postsynaptic potential / tertiary granule membrane / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / long-term memory / specific granule membrane / axonal growth cone / response to glucose / presynaptic active zone membrane / vesicle-mediated transport
Similarity search - Function
Single Helix bin / Synaphin / Synaphin protein / Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin ...Single Helix bin / Synaphin / Synaphin protein / Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Syntaxin-1A / Synaptosomal-associated protein 25 / Complexin-1 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, X. / Tomchick, D. / Kovrigin, E. / Arac, D. / Machius, M. / Sudhof, T.C. / Rizo, J.
CitationJournal: Neuron / Year: 2002
Title: Three-dimensional structure of the complexin/SNARE complex.
Authors: Chen, X. / Tomchick, D.R. / Kovrigin, E. / Arac, D. / Machius, M. / Sudhof, T.C. / Rizo, J.
History
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE RESIDUE 10 CHAIN C, THE WILD-TYPE SEQUENCE STARTS WITH LEU11. SER10 IN THE COORDINATES IS ... SEQUENCE RESIDUE 10 CHAIN C, THE WILD-TYPE SEQUENCE STARTS WITH LEU11. SER10 IN THE COORDINATES IS PART OF THE VECTOR GLY9 WHICH IS DISORDERED. RESIDUE 140 CHAIN D, THE WILD-TYPE SEQUENCE STARTS WITH ALA141. BOTH RESIDUES FROM THE VECTOR GLY139 AND SER140 ARE ORDERED. RESIDUE 204 CHAIN D IS AN ENGINEERED TRP(FLUORESCENCE STUDIES) IT IS NOT PART OF THE NATIVE SEQUENCES, THREFORE NOT A MUTATION.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptobrevin SNARE motif
B: Syntaxin SNARE motif short
C: SNAP-25 N-terminal SNARE motif
D: SNAP-25 C-terminal SNARE motif
E: Complexin I SNARE-complex binding region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9247
Polymers36,8755
Non-polymers492
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-113 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.489, 60.425, 159.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein Synaptobrevin SNARE motif / vesicle associated membrane protein 2B


Mass: 7660.553 Da / Num. of mol.: 1 / Fragment: SNARE motif (29-93)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Synaptobrevin 2 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63045
#2: Protein Syntaxin SNARE motif short / synaptotagmin associated associated 35 kDA protein


Mass: 7192.038 Da / Num. of mol.: 1 / Fragment: SNARE motif (191-253)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syntaxin 1A / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32851
#3: Protein SNAP-25 N-terminal SNARE motif / synaptosomal-associated protein 25kD


Mass: 8642.615 Da / Num. of mol.: 1 / Fragment: SNARE motif (11-82) / Mutation: W added at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP-25 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60880
#4: Protein SNAP-25 C-terminal SNARE motif / synaptosomal-associated protein 25kD


Mass: 7613.459 Da / Num. of mol.: 1 / Fragment: SNARE motif (141-203) / Mutation: W added at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP-25 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60880

-
Protein/peptide , 1 types, 1 molecules E

#5: Protein/peptide Complexin I SNARE-complex binding region


Mass: 5766.459 Da / Num. of mol.: 1 / Fragment: Complexin (residues 26-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Complexin 1 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63041

-
Non-polymers , 2 types, 115 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27%(v/v) Iso-Propanol, 200mM MgCl2, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.5
2130 mM1dropNaCl
310 mg/mlprotein1drop
435 %(v/v)isopropanol1reservoir
5200 mM1reservoirMgCl2
6100 mMHEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 20, 2001
RadiationMonochromator: Double-crystal monochrmator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→32.2 Å / Num. all: 18098 / Num. obs: 17624 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.3 / Num. unique all: 728 / Rsym value: 0.265 / % possible all: 82.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 14111 / % possible obs: 99.6 % / Num. measured all: 78881 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 6.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFC

1sfc


Resolution: 2.3→32.23 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1536401.45 / Data cutoff high rms absF: 1536401.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1005 6.3 %RANDOM
Rwork0.245 ---
all0.287 15857 --
obs-15857 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1732 Å2 / ksol: 0.32352 e/Å3
Displacement parametersBiso mean: 65.7 Å2
Baniso -1Baniso -2Baniso -3
1-36.42 Å20 Å20 Å2
2---4.39 Å20 Å2
3----32.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 2 113 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.932.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 116 5.7 %
Rwork0.361 1920 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.
X-RAY DIFFRACTION3ION.PARAMION.
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 13041 / σ(F): 0 / % reflection Rfree: 6.3 % / Rfactor obs: 0.237 / Rfactor Rfree: 0.303
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 65.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scangle_it3.932.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.361

+
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