[English] 日本語
Yorodumi
- PDB-3hn8: Crystal structure of synaptotagmin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hn8
TitleCrystal structure of synaptotagmin
ComponentsSynaptotagmin-3
KeywordsSIGNALING PROTEIN / synaptotagmin / Cell junction / Cytoplasmic vesicle / Membrane / Metal-binding / Synapse / Transmembrane
Function / homology
Function and homology information


positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / calcium-ion regulated exocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / transport vesicle membrane / phosphatidylserine binding ...positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / calcium-ion regulated exocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / transport vesicle membrane / phosphatidylserine binding / synaptic vesicle exocytosis / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatidylinositol-4,5-bisphosphate binding / SNARE binding / synaptic membrane / response to calcium ion / presynapse / postsynapse / cell differentiation / protein heterodimerization activity / calcium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsStrop, P. / Vrljic, M. / Ernst, J. / Brunger, A.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion.
Authors: Vrljic, M. / Strop, P. / Ernst, J.A. / Sutton, R.B. / Chu, S. / Brunger, A.T.
History
DepositionMay 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptotagmin-3
B: Synaptotagmin-3
C: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46324
Polymers99,5463
Non-polymers91821
Water00
1
A: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4888
Polymers33,1821
Non-polymers3067
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4888
Polymers33,1821
Non-polymers3067
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4888
Polymers33,1821
Non-polymers3067
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.675, 205.675, 143.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROchain A and (resseq 295:412 or resseq 414:573 )AA295 - 4124 - 121
12ARGARGSERSERchain A and (resseq 295:412 or resseq 414:573 )AA414 - 573123 - 282
21GLYGLYPROPROchain B and (resseq 295:412 or resseq 414:573 )BB295 - 4124 - 121
22ARGARGSERSERchain B and (resseq 295:412 or resseq 414:573 )BB414 - 573123 - 282
31GLYGLYPROPROchain C and (resseq 295:412 or resseq 414:573 )CC295 - 4124 - 121
32ARGARGSERSERchain C and (resseq 295:412 or resseq 414:573 )CC414 - 573123 - 282

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.044483, 0.998188, 0.040528), (-0.052226, -0.042836, 0.997716), (0.997644, 0.042265, 0.054037)-146.026001, 35.2094, 101.112999
3given(-0.071986, 0.014386, 0.997302), (-0.001424, -0.999896, 0.014321), (0.997405, -0.000389, 0.071999)-72.120499, 39.933399, 66.350899

-
Components

#1: Protein Synaptotagmin-3 / Synaptotagmin III / SytIII


Mass: 33181.852 Da / Num. of mol.: 3 / Fragment: UNP residues 292-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40748
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.6 Å3/Da / Density % sol: 83.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 17% MPD, 50mM CaCl2, 100mM NaCl, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 10.36 / Number: 228916 / Rmerge(I) obs: 0.167 / Χ2: 1.25 / D res high: 3.5 Å / D res low: 50 Å / Num. obs: 39136 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.535097.610.0440.9815.5
5.987.5399.810.1071.1555.9
5.235.9899.910.1431.1725.9
4.755.2399.910.1411.1826
4.414.7510010.1541.1846
4.154.4199.910.1981.2856
3.944.1510010.2961.3776
3.773.9499.810.4251.5885.5
3.633.7710010.4971.0555.8
3.53.6310010.5711.5895.9
ReflectionResolution: 3.5→50 Å / Num. all: 39136 / Num. obs: 39136 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.167 / Χ2: 1.255 / Net I/σ(I): 10.361
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.571 / Num. unique all: 3851 / Χ2: 1.589 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→29.816 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.802 / SU ML: -0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3927 10.06 %random
Rwork0.238 ---
all0.24 39055 --
obs0.24 39055 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.648 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso max: 257.56 Å2 / Biso mean: 90.786 Å2 / Biso min: 35.38 Å2
Baniso -1Baniso -2Baniso -3
1--20.984 Å2-0 Å20 Å2
2---20.984 Å2-0 Å2
3---41.969 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6651 0 21 0 6672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046806
X-RAY DIFFRACTIONf_angle_d0.9379228
X-RAY DIFFRACTIONf_chiral_restr0.0641029
X-RAY DIFFRACTIONf_plane_restr0.0051197
X-RAY DIFFRACTIONf_dihedral_angle_d25.1634197
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2209X-RAY DIFFRACTIONPOSITIONAL0.017
12B2209X-RAY DIFFRACTIONPOSITIONAL0.017
13C2209X-RAY DIFFRACTIONPOSITIONAL0.022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.5430.3421400.3191235137599
3.543-3.5880.3311460.3112121358100
3.588-3.6350.3421370.29512581395100
3.635-3.6850.331370.30112291366100
3.685-3.7370.3221390.29412321371100
3.737-3.7930.3431260.30112421368100
3.793-3.8520.2861480.28312191367100
3.852-3.9150.2671400.2731234137499
3.915-3.9820.3061220.28112611383100
3.982-4.0550.2881460.25412231369100
4.055-4.1320.2461560.2512161372100
4.132-4.2160.2631400.22212571397100
4.216-4.3080.2311440.22512331377100
4.308-4.4080.2351490.19812431392100
4.408-4.5180.1931390.18812341373100
4.518-4.6390.1911430.18512641407100
4.639-4.7750.1811130.17212611374100
4.775-4.9290.1831180.19312841402100
4.929-5.1040.2161420.1912481390100
5.104-5.3070.1871560.20412431399100
5.307-5.5480.2841160.22812741390100
5.548-5.8380.2951440.24412611405100
5.838-6.2010.3161490.24712611410100
6.201-6.6740.2371230.25412991422100
6.674-7.3370.2981590.23512641423100
7.337-8.3780.2291580.21512751433100
8.378-10.4790.1991290.17713311460100
10.479-29.8170.2781680.2841335150398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.499-0.564-0.58760.88630.60160.9494-0.07230.24820.0089-0.038-0.2014-0.04240.0006-0.16250.20810.61860.11910.05350.6825-0.14970.5171-61.809840.36550.5193
21.08660.1043-0.4061.195-0.12370.40660.1150.2457-0.64790.1358-0.1166-0.3335-0.0376-0.07190.02540.446-0.05140.14770.4974-0.19210.7234-64.361536.686724.8559
3-0.593-0.07451.08071.4073-0.34241.43480.07560.0560.2117-0.0753-0.42330.76990.0556-0.1790.20830.43020.0186-0.04080.7950.0230.7967-104.374479.59313.1155
40.81140.28030.25971.17350.952-0.2017-0.04940.1291-0.1039-0.3457-0.0826-0.0672-0.28540.13190.1660.53890.1090.00350.56080.00520.333-79.786978.22960.663
51.4511-0.37610.04370.74510.62221.12930.1927-0.10490.1268-0.00520.0420.13870.06490.0423-0.14340.53140.0368-0.08070.5235-0.22680.828-66.3983-0.2265.5432
60.4444-0.09130.22720.6685-0.46660.21550.08860.0651-0.24020.21420.053-0.2398-0.1430.029-0.14770.59090.08540.02660.5328-0.20740.6394-41.94183.37364.7038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 295:427A295 - 427
2X-RAY DIFFRACTION2chain A and resid 428:573A428 - 573
3X-RAY DIFFRACTION3chain B and resid 295:427B295 - 427
4X-RAY DIFFRACTION4chain B and resid 428:573B428 - 573
5X-RAY DIFFRACTION5chain C and resid 295:427C295 - 427
6X-RAY DIFFRACTION6chain C and resid 428:573C428 - 573

+
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