[English] 日本語
Yorodumi
- PDB-5kj7: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long u... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kj7
TitleStructure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction
Components
  • (Synaptosomal-associated protein ...) x 2
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 3
KeywordsENDOCYTOSIS / EXOCYTOSIS / XFEL STRUCTURE / SYNAPTIC FUSION COMPLEX / SYNAPTOTAGMIN1 / NEURONAL SNARE COMPLEX
Function / homology
Function and homology information


negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / : / RHOG GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / : / RHOH GTPase cycle ...negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / : / RHOG GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / : / RHOH GTPase cycle / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle / RAC1 GTPase cycle / BLOC-1 complex / RHOA GTPase cycle / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / calcium ion sensor activity / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / positive regulation of norepinephrine secretion / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / regulated exocytosis / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / regulation of establishment of protein localization / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / intracellular organelle / vesicle docking / regulation of calcium ion-dependent exocytosis / clathrin-coated vesicle membrane / exocytic vesicle / chloride channel inhibitor activity / Golgi to plasma membrane protein transport / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / secretion by cell / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / positive regulation of hormone secretion / neurotransmitter receptor internalization / neuron projection terminus / neurotransmitter transport / calcium-dependent phospholipid binding / ATP-dependent protein binding / protein localization to membrane / retrograde transport, endosome to Golgi / syntaxin-1 binding / insulin secretion / SNARE complex assembly / positive regulation of neurotransmitter secretion / low-density lipoprotein particle receptor binding / synaptic vesicle priming / syntaxin binding / Neutrophil degranulation / clathrin-coated vesicle / regulation of synapse assembly / endosomal transport / regulation of synaptic vesicle exocytosis / clathrin binding / myosin binding / positive regulation of receptor recycling / intracellular vesicle / phosphatidylserine binding / regulation of dopamine secretion
Similarity search - Function
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 ...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 / Synaptotagmin / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Synaptotagmin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsLyubimov, A.Y. / Uervirojnangkoorn, M. / Zhou, Q. / Zhao, M. / Sauter, N.K. / Brewster, A.S. / Weis, W.I. / Brunger, A.T.
Funding support United States, 3items
OrganizationGrant numberCountry
Hughes Collaborative Innovation Award United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102520 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117126 United States
CitationJournal: Elife / Year: 2016
Title: Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.
Authors: Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Zhou, Q. / Zhao, M. / Brewster, A.S. / Michels-Clark, T. / Holton, J.M. / Sauter, N.K. / Weis, W.I. / Brunger, A.T.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_data_reduction ...diffrn / pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery_fixed_target
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 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_ncs_dom_lim
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vesicle-associated membrane protein 3
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
G: Vesicle-associated membrane protein 3
H: Syntaxin-1A
I: Synaptosomal-associated protein 25
J: Synaptosomal-associated protein 25
K: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,76730
Polymers158,00611
Non-polymers76119
Water30617
1
A: Vesicle-associated membrane protein 3
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,40915
Polymers63,0095
Non-polymers40110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1495
Polymers31,9891
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Vesicle-associated membrane protein 3
H: Syntaxin-1A
I: Synaptosomal-associated protein 25
J: Synaptosomal-associated protein 25
K: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,20910
Polymers63,0095
Non-polymers2005
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.386, 170.676, 291.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain E and (resseq 143:172 or (resid 173 and (name...
21(chain K and (resseq 143:172 or (resid 173 and (name...
12(chain A and (resseq 27:29 or (resid 30 and (name...
22(chain G and (resseq 27:32 or (resid 33 and (name...
13(chain C and (resseq 11:12 or (resid 13 and (name...
23(chain I and (resseq 11:58 or resseq 60:78 or (resid...
14(chain B and (resseq 191:197 or (resid 198 and (name...
24(chain H and (resseq 191:209 or resseq 211:227 or (resid...
15(chain D and (resseq 144:160 or (resid 161 and (name...
25(chain J and (resseq 144:161 or resseq 163:190 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYASPASP(chain E and (resseq 143:172 or (resid 173 and (name...EE143 - 1723 - 32
121METMETMETMET(chain E and (resseq 143:172 or (resid 173 and (name...EE17333
131LYSLYSVALVAL(chain E and (resseq 143:172 or (resid 173 and (name...EE141 - 4191 - 279
141LYSLYSVALVAL(chain E and (resseq 143:172 or (resid 173 and (name...EE141 - 4191 - 279
211GLYGLYASPASP(chain K and (resseq 143:172 or (resid 173 and (name...KK143 - 1723 - 32
221METMETMETMET(chain K and (resseq 143:172 or (resid 173 and (name...KK17333
231LYSLYSVALVAL(chain K and (resseq 143:172 or (resid 173 and (name...KK141 - 4191 - 279
241LYSLYSVALVAL(chain K and (resseq 143:172 or (resid 173 and (name...KK141 - 4191 - 279
112GLYGLYASNASN(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 291 - 3
122ARGARGARGARG(chain A and (resseq 27:29 or (resid 30 and (name...AA304
132GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
142GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
152GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
162GLYGLYTRPTRP(chain A and (resseq 27:29 or (resid 30 and (name...AA27 - 891 - 63
212GLYGLYLEULEU(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 321 - 6
222GLNGLNGLNGLN(chain G and (resseq 27:32 or (resid 33 and (name...GG337
232GLYGLYTRPTRP(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 891 - 63
242GLYGLYTRPTRP(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 891 - 63
252GLYGLYTRPTRP(chain G and (resseq 27:32 or (resid 33 and (name...GG27 - 891 - 63
113LEULEUGLUGLU(chain C and (resseq 11:12 or (resid 13 and (name...CC11 - 123 - 4
123GLUGLUGLUGLU(chain C and (resseq 11:12 or (resid 13 and (name...CC135
133ASNASNGLYGLY(chain C and (resseq 11:12 or (resid 13 and (name...CC9 - 821 - 74
143ASNASNGLYGLY(chain C and (resseq 11:12 or (resid 13 and (name...CC9 - 821 - 74
153ASNASNGLYGLY(chain C and (resseq 11:12 or (resid 13 and (name...CC9 - 821 - 74
213LEULEUASPASP(chain I and (resseq 11:58 or resseq 60:78 or (resid...II11 - 583 - 50
223VALVALLEULEU(chain I and (resseq 11:58 or resseq 60:78 or (resid...II60 - 7852 - 70
233LYSLYSLYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II7971
243GLUGLULYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II10 - 832 - 75
253GLUGLULYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II10 - 832 - 75
263GLUGLULYSLYS(chain I and (resseq 11:58 or resseq 60:78 or (resid...II10 - 832 - 75
114ALAALATHRTHR(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 1971 - 7
124ARGARGARGARG(chain B and (resseq 191:197 or (resid 198 and (name...BB1988
134ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
144ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
154ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
164ALAALALYSLYS(chain B and (resseq 191:197 or (resid 198 and (name...BB191 - 2561 - 66
214ALAALAILEILE(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2091 - 19
224GLUGLUGLYGLY(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH211 - 22721 - 37
234GLUGLUGLUGLU(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH22838
244ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
254ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
264ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
274ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
284ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
294ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
2104ALAALAVALVAL(chain H and (resseq 191:209 or resseq 211:227 or (resid...HH191 - 2551 - 65
115ASNASNLEULEU(chain D and (resseq 144:160 or (resid 161 and (name...DD144 - 1604 - 20
125ARGARGARGARG(chain D and (resseq 144:160 or (resid 161 and (name...DD16121
135ALAALAGLYGLY(chain D and (resseq 144:160 or (resid 161 and (name...DD141 - 2041 - 64
145ALAALAGLYGLY(chain D and (resseq 144:160 or (resid 161 and (name...DD141 - 2041 - 64
155ALAALAGLYGLY(chain D and (resseq 144:160 or (resid 161 and (name...DD141 - 2041 - 64
215ASNASNARGARG(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ144 - 1614 - 21
225METMETTHRTHR(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ163 - 19023 - 50
235ILEILEASNASN(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ192 - 19652 - 56
245GLNGLNGLNGLN(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ19757
255ALAALALEULEU(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ141 - 2031 - 63
265ALAALALEULEU(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ141 - 2031 - 63
275ALAALALEULEU(chain J and (resseq 144:161 or resseq 163:190 or resseq...JJ141 - 2031 - 63

NCS ensembles :
ID
1
2
3
4
5

-
Components

-
Protein , 3 types, 7 molecules AGBHEFK

#1: Protein Vesicle-associated membrane protein 3 / VAMP-3 / Cellubrevin / CEB / Synaptobrevin-3


Mass: 7231.061 Da / Num. of mol.: 2 / Fragment: UNP residues 14-76
Source method: isolated from a genetically manipulated source
Details: 96% helical (1 helices; 61 residues) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp3, Syb3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63025
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7706.761 Da / Num. of mol.: 2 / Fragment: UNP residues 191-256
Source method: isolated from a genetically manipulated source
Details: 91% helical (1 helices; 61 residues) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#5: Protein Synaptotagmin-1 / / Synaptotagmin I / SytI / p65


Mass: 31988.838 Da / Num. of mol.: 3 / Fragment: UNP residues 141-419
Source method: isolated from a genetically manipulated source
Details: 9% helical (5 helices; 27 residues) 45% beta sheet (19 strands; 129 residues)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707

-
Synaptosomal-associated protein ... , 2 types, 4 molecules CIDJ

#3: Protein Synaptosomal-associated protein 25 / SNAP25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 8741.725 Da / Num. of mol.: 2 / Fragment: UNP residues 9-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 7340.173 Da / Num. of mol.: 2 / Fragment: UNP residues 141- 204
Source method: isolated from a genetically manipulated source
Details: 92% helical (1 helices; 60 residues) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881

-
Non-polymers , 2 types, 36 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 5.45 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.307 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.307 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 43622 / % possible obs: 97.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 66.8 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.494 / Net I/σ(I): 3.6
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 0.2 / % possible all: 89.2
Serial crystallography measurementFocal spot size: 30 µm2 / Photons per pulse: 1 Tphotons/pulse / Pulse duration: 40 fsec. / Pulse photon energy: 9 keV
Serial crystallography sample delivery fixed targetMotion control: DCSS / Sample holding: cryo-loop
Sample solvent: 100 mM Tris-HCl (pH 8.5), 1.5 M ammonium sulfate
Support base: goniometer
Serial crystallography data reductionCrystal hits: 578 / Frames indexed: 309 / Frames total: 799

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S, 3F04, 1UOW

1n7s

3f04

1uow


Resolution: 3.5→19.956 Å / SU ML: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.2
RfactorNum. reflection% reflection
Rfree0.3291 2083 5.14 %
Rwork0.292 --
obs0.2939 40510 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 240.46 Å2 / Biso mean: 106 Å2 / Biso min: 26.94 Å2
Refinement stepCycle: final / Resolution: 3.5→19.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 19 17 10578
Biso mean--87.67 44.31 -
Num. residues----1365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210701
X-RAY DIFFRACTIONf_angle_d0.4514435
X-RAY DIFFRACTIONf_chiral_restr0.0371596
X-RAY DIFFRACTIONf_plane_restr0.0031919
X-RAY DIFFRACTIONf_dihedral_angle_d13.9416431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11E2310X-RAY DIFFRACTION7.588TORSIONAL
12K2310X-RAY DIFFRACTION7.588TORSIONAL
21A572X-RAY DIFFRACTION7.588TORSIONAL
22G572X-RAY DIFFRACTION7.588TORSIONAL
31C596X-RAY DIFFRACTION7.588TORSIONAL
32I596X-RAY DIFFRACTION7.588TORSIONAL
41B538X-RAY DIFFRACTION7.588TORSIONAL
42H538X-RAY DIFFRACTION7.588TORSIONAL
51D508X-RAY DIFFRACTION7.588TORSIONAL
52J508X-RAY DIFFRACTION7.588TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.5810.4616530.391891096333
3.581-3.67010.44191140.3912033214773
3.6701-3.76860.37521140.3872199231380
3.7686-3.87880.40871430.37662683282695
3.8788-4.0030.43051440.36432651279597
4.003-4.14480.33651480.34732726287498
4.1448-4.30920.40091480.32912737288598
4.3092-4.50320.39511460.32012723286998
4.5032-4.73760.33281510.29992759291099
4.7376-5.030.32731500.27252755290599
5.03-5.41110.34261510.2782783293499
5.4111-5.94260.29291520.291828122964100
5.9426-6.77290.37631520.29682811296399
6.7729-8.42490.2881560.25312864302099
8.4249-19.95640.21941610.216829813142100

+
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