[English] 日本語
Yorodumi
- PDB-7bv6: Crystal structure of the autophagic STX17/SNAP29/VAMP8 SNARE complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bv6
TitleCrystal structure of the autophagic STX17/SNAP29/VAMP8 SNARE complex
Components
  • (Synaptosomal-associated protein 29) x 2
  • Syntaxin-17
  • Vesicle-associated membrane protein 8
KeywordsSIGNALING PROTEIN / Autophagy / Synatxin 17 / GABARAP
Function / homology
Function and homology information


endoplasmic reticulum-Golgi intermediate compartment organization / mucin granule / negative regulation of secretion by cell / ciliary pocket membrane / positive regulation of histamine secretion by mast cell / smooth endoplasmic reticulum membrane / vesicle targeting / trans-Golgi Network Vesicle Budding / synaptic vesicle fusion to presynaptic active zone membrane / mitochondria-associated endoplasmic reticulum membrane contact site ...endoplasmic reticulum-Golgi intermediate compartment organization / mucin granule / negative regulation of secretion by cell / ciliary pocket membrane / positive regulation of histamine secretion by mast cell / smooth endoplasmic reticulum membrane / vesicle targeting / trans-Golgi Network Vesicle Budding / synaptic vesicle fusion to presynaptic active zone membrane / mitochondria-associated endoplasmic reticulum membrane contact site / Intra-Golgi traffic / mucus secretion / vesicle fusion / vesicle docking / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / protein localization to phagophore assembly site / SNARE complex assembly / COPII-mediated vesicle transport / synaptic vesicle priming / syntaxin binding / Lysosome Vesicle Biogenesis / azurophil granule membrane / autophagosome membrane docking / Golgi Associated Vesicle Biogenesis / COPII-coated ER to Golgi transport vesicle / Golgi organization / exocytosis / autophagosome maturation / autophagosome membrane / tertiary granule membrane / cilium assembly / endoplasmic reticulum-Golgi intermediate compartment / autophagosome / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / specific granule membrane / regulation of protein localization to plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / SNARE binding / secretory granule membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / late endosome membrane / ER-Phagosome pathway / early endosome membrane / protein phosphatase binding / defense response to virus / vesicle / membrane fusion / early endosome / symbiont entry into host cell / lysosomal membrane / Golgi membrane / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntaxin-17 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Syntaxin / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. ...Syntaxin-17 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Syntaxin / 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
Similarity search - Domain/homology
Synaptosomal-associated protein 29 / Syntaxin-17 / Vesicle-associated membrane protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLi, Y. / Pan, L.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470749 China
National Natural Science Foundation of China (NSFC)21621002 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Decoding three distinct states of the Syntaxin17 SNARE motif in mediating autophagosome-lysosome fusion.
Authors: Li, Y. / Cheng, X. / Li, M. / Wang, Y. / Fu, T. / Zhou, Z. / Wang, Y. / Gong, X. / Xu, X. / Liu, J. / Pan, L.
History
DepositionApr 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vesicle-associated membrane protein 8
B: Syntaxin-17
C: Synaptosomal-associated protein 29
D: Synaptosomal-associated protein 29
E: Vesicle-associated membrane protein 8
F: Syntaxin-17
G: Synaptosomal-associated protein 29
H: Synaptosomal-associated protein 29
I: Vesicle-associated membrane protein 8
J: Syntaxin-17
K: Synaptosomal-associated protein 29
L: Synaptosomal-associated protein 29
M: Vesicle-associated membrane protein 8
N: Syntaxin-17
O: Synaptosomal-associated protein 29
P: Synaptosomal-associated protein 29
Q: Vesicle-associated membrane protein 8
R: Syntaxin-17
S: Synaptosomal-associated protein 29
T: Synaptosomal-associated protein 29
U: Vesicle-associated membrane protein 8
V: Syntaxin-17
W: Synaptosomal-associated protein 29
X: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)214,54324
Polymers214,54324
Non-polymers00
Water0
1
A: Vesicle-associated membrane protein 8
B: Syntaxin-17
C: Synaptosomal-associated protein 29
D: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)35,7574
Polymers35,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-98 kcal/mol
Surface area14000 Å2
MethodPISA
2
E: Vesicle-associated membrane protein 8
F: Syntaxin-17
G: Synaptosomal-associated protein 29
H: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)35,7574
Polymers35,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-102 kcal/mol
Surface area14310 Å2
MethodPISA
3
I: Vesicle-associated membrane protein 8
J: Syntaxin-17
K: Synaptosomal-associated protein 29
L: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)35,7574
Polymers35,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-99 kcal/mol
Surface area14310 Å2
MethodPISA
4
M: Vesicle-associated membrane protein 8
N: Syntaxin-17
O: Synaptosomal-associated protein 29
P: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)35,7574
Polymers35,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-102 kcal/mol
Surface area14470 Å2
MethodPISA
5
Q: Vesicle-associated membrane protein 8
R: Syntaxin-17
S: Synaptosomal-associated protein 29
T: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)35,7574
Polymers35,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-85 kcal/mol
Surface area13780 Å2
MethodPISA
6
U: Vesicle-associated membrane protein 8
V: Syntaxin-17
W: Synaptosomal-associated protein 29
X: Synaptosomal-associated protein 29


Theoretical massNumber of molelcules
Total (without water)35,7574
Polymers35,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-104 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.981, 196.000, 76.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein
Vesicle-associated membrane protein 8 / / VAMP-8 / Endobrevin / EDB


Mass: 7980.967 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAMP8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BV40
#2: Protein
Syntaxin-17 /


Mass: 9494.307 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STX17 / Production host: Escherichia coli (E. coli) / References: UniProt: P56962
#3: Protein
Synaptosomal-associated protein 29 / SNAP-29 / Soluble 29 kDa NSF attachment protein / Vesicle-membrane fusion protein SNAP-29


Mass: 10379.804 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP29 / Production host: Escherichia coli (E. coli) / References: UniProt: O95721
#4: Protein
Synaptosomal-associated protein 29 / SNAP-29 / Soluble 29 kDa NSF attachment protein / Vesicle-membrane fusion protein SNAP-29


Mass: 7902.030 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP29 / Production host: Escherichia coli (E. coli) / References: UniProt: O95721

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2.5 M Ammonium nitrate, 0.1 M Sodium acetate trihydrate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 41797 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.56 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.3
Reflection shellResolution: 3.05→3.1 Å / CC1/2: 0.93

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GL2

1gl2


Resolution: 3.05→49 Å / SU ML: 0.4024 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2647
RfactorNum. reflection% reflection
Rfree0.2554 2085 4.99 %
Rwork0.1751 --
obs0.1792 41796 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62.3 Å2
Refinement stepCycle: LAST / Resolution: 3.05→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12345 0 0 0 12345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912427
X-RAY DIFFRACTIONf_angle_d0.998616705
X-RAY DIFFRACTIONf_chiral_restr0.05011976
X-RAY DIFFRACTIONf_plane_restr0.00452172
X-RAY DIFFRACTIONf_dihedral_angle_d25.07651668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.120.35561480.24462596X-RAY DIFFRACTION99.89
3.12-3.20.33851450.23472604X-RAY DIFFRACTION99.82
3.2-3.290.29581390.23422591X-RAY DIFFRACTION99.93
3.29-3.380.30341420.1972608X-RAY DIFFRACTION99.85
3.38-3.490.28731190.18322640X-RAY DIFFRACTION99.93
3.49-3.620.24411400.17912640X-RAY DIFFRACTION99.96
3.62-3.760.26911480.18382600X-RAY DIFFRACTION99.89
3.76-3.930.25751420.17682614X-RAY DIFFRACTION99.93
3.93-4.140.22921430.15952624X-RAY DIFFRACTION99.64
4.14-4.40.24471250.13542660X-RAY DIFFRACTION100
4.4-4.740.21221430.14392658X-RAY DIFFRACTION100
4.74-5.210.24451370.15662665X-RAY DIFFRACTION99.79
5.21-5.970.34951410.23082682X-RAY DIFFRACTION100
5.97-7.510.28361490.1942712X-RAY DIFFRACTION99.86
7.51-490.16731240.14232817X-RAY DIFFRACTION97.94
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)
11.187864358840.3689579298170.1745876036152.62993712862-0.0443297154280.673070257345-0.0152913768593-0.121224396851-0.0823783821138-0.3335729335690.0458143391692-0.7092658832140.0800728185987-0.0130715564021-0.05245547934890.256578155205-0.00312263838760.03339809471940.37881107882-0.0004264068337960.153938597521-16.29873260590.266045366901-27.9034783545
20.5516115976220.243689989497-0.5010952042673.14244939462-1.659188496470.875596133857-0.0556704630037-0.195814150937-0.00086712424445-0.807076167684-0.02957584391480.750619343360.0910298899201-0.0326638731920.02204303025610.236734041068-0.0542249497745-0.01670485640860.3554929940290.05293424884880.272347224049-19.98736977834.68761290296-31.6425067552
30.723212851145-0.8001750256280.1316587367143.06522561302-0.273669976230.254231923088-0.274973080363-0.0339207024645-0.0924897820721-0.4025422016010.4118383653530.150733007920.102669640863-0.175134904114-0.03814159873520.3392349290150.05433746697620.03635158984680.343509976551-0.03151402755270.272277996043-24.323388954912.1214615621-28.5383745394
40.930955835198-1.09858544041-0.1469423602128.99907408933-0.6999183431110.396468202976-0.145422283274-0.06333503853960.0582439490205-0.02827046500110.291809665539-0.135492139307-0.006345446793620.0363357253743-0.09438464128760.3530519894110.01262210705680.04834281428560.302608517027-0.002488728706510.270183386278-21.075692158312.5382396868-23.8801230851
51.725391315351.923368579710.5223283200388.463511885650.6767332639720.760490846425-0.146562855737-0.05271744838480.342973934846-0.4647748138080.07697501330811.09765018128-0.136651091746-0.2000672718540.06341649367270.2587802087190.06117612762450.03103869797330.412227553571-0.03502870513970.0728625313328-46.505184157519.439185927-64.4928948829
62.137859333032.055467818841.086045073582.771959898191.612885715621.22047053555-0.4779572609120.289423088212-0.0490158550923-0.6714879842710.709578548626-0.385213205841-0.304943078980.0137436888316-0.2347377494130.345564243781-0.0241483639920.01322197336010.3439033805350.002777587456070.208141283765-43.470493154213.8417980477-68.4913441
70.802736382060.8193782192630.2827174053178.958763419622.944364166651.77982036928-0.18592824467-0.00662563598883-0.146430359253-0.3027945105780.344495821884-0.0766592451969-0.1813628307290.186395520418-0.09591161120020.2923186756190.0940609887542-0.1031490715180.3263867698780.07065770733080.221840339159-40.78871029363.73600459427-66.712452122
81.09087481053-0.2529969493230.005320691516327.890559047552.92279820461.4638998912-0.0718722634502-0.1149994674430.05666214143350.4368686161590.2378341992850.0908531132180.2228931452140.0701431274519-0.1638494245250.2948417070420.0335125357033-0.01812214665890.4380048435670.01387610493570.217386190854-43.34068855374.75475984505-62.4857901654
95.559673232954.99336790663-2.079862782756.87262028539-2.316110683631.88357136873-0.1054978169790.5994672132790.157909180563-0.0645489599160.3844959994720.0259199895868-0.0700584910068-0.127404504273-0.2025127678930.2223539961650.07893460124530.01844844500890.428481837067-0.04374819804870.240459401939-53.273198777711.0277478271-89.1789802489
100.1036273986070.2528432400040.2341836005221.435142651731.086442274480.8394526608820.896813963056-0.06873705121460.0570556225711.71671065868-0.0677675248085-0.2034926657-0.4063556865690.575847231702-0.5287505504271.66138428746-0.6150074789150.1506054955880.877732723420.03953417919691.61922941511-28.887010705153.5437701964-89.5503070302
111.875660657773.11081623008-0.8488572997468.62397737485-1.099765602081.422149499140.575184047526-0.0738104088916-0.1303546428140.961766544162-0.491352289661-0.651663973787-0.493048855750.0545968245223-0.08197054621180.3491721291990.02152117288150.03692153809480.31285117009-0.03738506500860.324036333345-48.98077031214.8265862369-83.2310648376
120.04476173208670.0006925625379380.02521498288560.0363680555912-0.001267684667850.0103733102369-0.527481396640.694377234565-0.00842841086672-0.8685551209160.223791424138-0.2903496292110.4400424122451.47329693470.1903900832681.041824980270.102455940631-0.09912910284731.42033440137-0.5239903704481.07123336324-67.4257462716-34.3222226174-69.759736343
132.48434085542.65858548964-1.507151999178.97621244739-3.00270165461.915256344890.2575653710880.1283493576010.3978333241170.2110570376360.0194068020730.38498799823-0.2764036616820.00250623679603-0.2619688795440.2812004274810.08589385235330.04547742608510.4267201329590.06054239072820.286216118614-54.590488513918.4113499418-81.2898616843
143.842133319724.29321413029-1.649700818129.68024420077-3.714260356182.37674033658-0.213089895370.5569383809990.226381028140.01164059901820.5688442401660.308305372052-0.0649053937204-0.460409380909-0.2793433325870.2228998432980.08441726847320.03670948845780.393711103364-0.03125467530910.228873464858-58.811706051212.4203420312-84.4676995566
154.432942524192.340558958031.332493648388.045783127091.021659207110.8402831286090.0474441851056-0.375609419093-0.4802432968960.3515773549190.10487356868-1.34168407971-0.058936445990.144069819444-0.0224546593880.3365139454620.0173688936783-0.006181006079280.437422740581-0.07913857828430.125845972746-30.34415379975.28968448686-79.729122042
164.18524585847-4.7018942660.8706263134715.30747882649-1.173065186873.311224137040.3008034927910.463033151629-0.178823475813-0.676351358271-0.117556829155-0.815148442519-0.194786559428-1.39210202817-0.09721208988280.8475986364160.0663528451431-0.2771543599350.8378934473330.08577430368522.10855715308-11.068820960548.6193150046-71.7060445105
174.818099943025.209138554810.5000862415728.05268748655-0.05660352747430.9126243345170.287179453717-0.02963393369990.698457904860.7273407221-0.2728965566970.45799212612-0.0724920664352-0.00476233261181-0.1106236394930.2425617052460.0642627176369-0.04758526238490.276931913888-0.03283687187840.411159980168-34.616455810410.1039723371-81.1809048403
184.299038142232.574576987881.491109500575.09602433291.434545590621.532255786450.02561285667250.5942900032450.4047159429680.04468445389660.244683703470.4166452607230.00473370966770.0765593133139-0.2210934092310.2380210046770.02684590372980.06597972521470.437095297598-0.02902987756030.120003485977-42.76582696120.397370464702-89.7668046514
190.200558872701-0.5678786375-1.053837599931.991550842752.251214467486.550997206860.90052694148-0.4081357305390.0196672408637-0.8617183169750.152371880613-0.601039965483-1.21032329258-0.217066998771-0.7007688656030.5862675965280.09622043217750.2361369015610.878336233829-0.2630953896572.19073982584-4.4003464220236.0728086415-81.3426127149
203.563904906110.27954898237-0.07542816519943.301332633830.4745251433810.84264898950.210814036240.350904293024-0.3978202087650.5035066709510.224120177888-0.6586947898820.2451734895120.155633103176-0.3071010714520.302612400972-0.0108416623790.02032749730810.2838120340610.04046940064550.149719278612-32.31732487013.01963582669-87.9416073177
214.357716162532.87483111699-0.1446517192018.550517445632.4034217272.78133352373-0.4973174980381.079722180450.0479064713369-0.6370046637980.5711791709150.559412204421-0.00159434012810.0604246024465-0.03604223349580.3048815679910.0637268795597-0.03594300240670.5754705052440.04649258219480.21423300935-9.9327825319811.4291944941-50.7832322902
220.543605302330.6457399379310.6211421306670.7597810471450.7321447798170.695827299056-0.608103911143-0.5690616736240.6263128512920.418272899198-0.8034195844030.3645311728370.111741556191-0.1732376429540.8340048115291.34150979498-0.0306097522364-0.2888565585160.908312825729-0.3003129091342.29046925803-30.0821515464-28.4470750216-59.9039538129
233.049971205141.461476150430.9044844308549.505941020632.244056397511.635820158870.1612915613990.236206580022-0.1032494672450.772189559865-0.131440840519-0.09778510086730.341776067814-0.3048209141020.03214870703650.414530644193-0.04954286424360.06988786189080.4032126499160.05273349549620.157744277596-12.550834058814.2082048265-43.7553676453
241.245875131470.03296523103221.60376425917-0.0007231599060720.03412975911972.08816049592-0.0127767723884-0.650590572618-0.379784868087-0.6932999093910.691598172609-0.8252397366071.604165382661.12812317582-0.2907032664371.15217166047-0.2893844610970.5214528365381.13470691585-0.7345391284231.40703048186-20.8896348238-24.8270609667-53.0808417308
252.317555523631.255543494240.332185436788.895736422693.805601833683.36113537075-0.1300194709040.255622475353-0.05137605127980.480918539851-0.2090388086340.3375170896480.467049130726-0.2177606506140.1189881738090.2678587187090.02821794939610.03362842601840.3997416268580.03580662951280.258819841726-7.0442374425110.249327397-41.1363306339
262.770778782971.561734921830.4512114790624.262014747271.536164898152.10451267047-0.1860406631750.6197368249760.0930635591483-0.07096866434960.245932795446-0.1760216386310.3719765323990.318281170021-0.1062089954410.3980178275230.0235016212087-0.0125014898090.4039623931150.04586127283540.198925569543-4.1896930360110.0946815091-45.3653050553
273.29111756333.19221739328-0.6053464354088.72190064889-0.9635893267831.015315798640.162115787861-0.0452457236718-0.09547820940380.650981581813-0.1094515929850.570396645072-0.0604982891163-0.0963434957666-0.1309523101830.2395933940610.0619703748062-0.06163502027310.3812046869130.09666177234470.291205094472-36.06449981087.86554210591-42.032914473
284.549265476563.95619919990.4891286221947.35761395638-0.1450874361110.519195239556-0.1727841267640.532349257731-0.1630756040310.01307580091560.4643364208470.1297729462610.04936510905290.00215941850566-0.3388680034410.3673533402950.05226363729360.01715857244930.3683137794010.03914619370830.24425621044-29.51350955759.62532009803-43.9380463137
296.847322242416.92091703667-0.6702733942729.4422108664-0.8091504643040.994390325418-0.1062503695440.365905760604-0.415550035785-0.109132043410.153532331243-0.573102592978-0.07279346375160.106637456951-0.05708993413850.2826361417030.0140196736558-0.01770948448490.4205199453620.08126712594340.276528479796-22.418731554520.108594471-50.5224636688
301.235193827780.9337287226831.308346998490.6956851758251.033516508166.155257995170.105918860893-0.411726541462-0.439947035731-0.455150533228-0.1093928189920.3773786717480.802457547463-1.395997393440.01748638700290.642444126152-0.0531783970182-0.3167279662310.5481234374030.1680554884681.75016444252-58.0128455324-17.9340240532-47.2786208829
310.1754752135-0.1400820355530.3466243864265.20310449791-2.401740289223.35821078961-0.2050969573230.3725050159140.188850392943-0.76933375168-0.151483221146-0.6435764107620.1399507085170.5203141513580.07107336260181.577578899950.005629373484640.2466160942871.084411805530.407334936930.7992879055371.2786919432944.5110475399-57.9871827738
325.610553971132.93641148411-0.07077620903365.15599761693-0.980985804280.798633557748-0.1158513619370.9784469495640.6314861211430.1982371986750.4902558497630.915908883675-0.0300538951188-0.253380043824-0.3325534723220.3795658672580.0155851741470.07150069420240.392118493691-0.03364240924070.177118558406-34.986216841314.8611737734-48.5499996445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 74 )
2X-RAY DIFFRACTION2chain 'B' and (resid 168 through 228 )
3X-RAY DIFFRACTION3chain 'C' and (resid 43 through 114 )
4X-RAY DIFFRACTION4chain 'D' and (resid 192 through 258 )
5X-RAY DIFFRACTION5chain 'E' and (resid 10 through 74 )
6X-RAY DIFFRACTION6chain 'F' and (resid 168 through 228 )
7X-RAY DIFFRACTION7chain 'G' and (resid 41 through 114 )
8X-RAY DIFFRACTION8chain 'H' and (resid 191 through 258 )
9X-RAY DIFFRACTION9chain 'I' and (resid 9 through 60 )
10X-RAY DIFFRACTION10chain 'I' and (resid 61 through 74 )
11X-RAY DIFFRACTION11chain 'J' and (resid 168 through 226 )
12X-RAY DIFFRACTION12chain 'K' and (resid 42 through 50 )
13X-RAY DIFFRACTION13chain 'K' and (resid 51 through 114 )
14X-RAY DIFFRACTION14chain 'L' and (resid 192 through 258 )
15X-RAY DIFFRACTION15chain 'M' and (resid 9 through 66 )
16X-RAY DIFFRACTION16chain 'M' and (resid 67 through 74 )
17X-RAY DIFFRACTION17chain 'N' and (resid 168 through 227 )
18X-RAY DIFFRACTION18chain 'O' and (resid 42 through 104 )
19X-RAY DIFFRACTION19chain 'O' and (resid 105 through 114 )
20X-RAY DIFFRACTION20chain 'P' and (resid 194 through 258 )
21X-RAY DIFFRACTION21chain 'Q' and (resid 9 through 59 )
22X-RAY DIFFRACTION22chain 'Q' and (resid 60 through 69 )
23X-RAY DIFFRACTION23chain 'R' and (resid 168 through 213 )
24X-RAY DIFFRACTION24chain 'R' and (resid 214 through 222 )
25X-RAY DIFFRACTION25chain 'S' and (resid 41 through 114 )
26X-RAY DIFFRACTION26chain 'T' and (resid 191 through 257 )
27X-RAY DIFFRACTION27chain 'U' and (resid 9 through 74 )
28X-RAY DIFFRACTION28chain 'V' and (resid 168 through 227 )
29X-RAY DIFFRACTION29chain 'W' and (resid 43 through 104 )
30X-RAY DIFFRACTION30chain 'W' and (resid 105 through 114 )
31X-RAY DIFFRACTION31chain 'X' and (resid 194 through 198 )
32X-RAY DIFFRACTION32chain 'X' and (resid 199 through 258 )

+
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