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- PDB-6k8j: Structure of NLRC4 CARD filament -

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Basic information

Entry
Database: PDB / ID: 6k8j
TitleStructure of NLRC4 CARD filament
ComponentsNLR family CARD domain-containing protein 4
KeywordsSIGNALING PROTEIN / filament
Function / homology
Function and homology information


IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / caspase binding / positive regulation of protein processing / activation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis ...IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / caspase binding / positive regulation of protein processing / activation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis / endopeptidase activator activity / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / protein homooligomerization / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of NF-kappaB transcription factor activity / defense response to bacterium / inflammatory response / positive regulation of apoptotic process / innate immune response / intracellular membrane-bounded organelle / apoptotic process / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NLR family CARD domain-containing protein 4 / NLRC4, helical domain / NLRC4 helical domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily ...NLR family CARD domain-containing protein 4 / NLRC4, helical domain / NLRC4 helical domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NLR family CARD domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGong, Q. / Xu, C. / Zhang, J. / Boo, Z.Z. / Wu, B.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)tier2 and tier1 Singapore
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8.
Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / ...Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / John Soon Yew Lim / Wah Ing Goh / Graham Wright / Franklin L Zhong / Bruno Reversade / Bin Wu /
Abstract: Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 ...Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIIND-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIIND-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIIND. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells-a process that is greatly enhanced by NLRP1-FIIND which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.
History
DepositionJun 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
G: NLR family CARD domain-containing protein 4
L: NLR family CARD domain-containing protein 4
K: NLR family CARD domain-containing protein 4
J: NLR family CARD domain-containing protein 4
I: NLR family CARD domain-containing protein 4
H: NLR family CARD domain-containing protein 4
F: NLR family CARD domain-containing protein 4
E: NLR family CARD domain-containing protein 4
D: NLR family CARD domain-containing protein 4
C: NLR family CARD domain-containing protein 4
B: NLR family CARD domain-containing protein 4
A: NLR family CARD domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)139,20512
Polymers139,20512
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
NLR family CARD domain-containing protein 4 / CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing ...CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing protein 12 / Ice protease-activating factor / Ipaf


Mass: 11600.412 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRC4, CARD12, CLAN, CLAN1, IPAF, UNQ6189/PRO20215 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9NPP4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: NLRC4 CARD filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Bl21(DE3)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2109
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: (dev_2405: ???) / Classification: refinement
EM software
IDNameVersionCategory
1RELION2particle selection
2EPU2.3image acquisition
4RELION2CTF correction
7Coot0.8.9.1 ELmodel fitting
9PHENIXdev 2405model refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -100.55 ° / Axial rise/subunit: 5.17 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 382715
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120602 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementResolution: 3.3→82.5 Å / SU ML: 1.15 / σ(F): 0.01 / Phase error: 51.13 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3057 1505 4.12 %
Rwork0.2571 --
obs0.2593 36562 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028472
ELECTRON MICROSCOPYf_angle_d0.36411376
ELECTRON MICROSCOPYf_dihedral_angle_d11.7825208
ELECTRON MICROSCOPYf_chiral_restr0.0371284
ELECTRON MICROSCOPYf_plane_restr0.0031440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.40650.58241400.59283117ELECTRON MICROSCOPY100
3.4065-3.52830.60361360.5853265ELECTRON MICROSCOPY100
3.5283-3.66950.57731480.5593153ELECTRON MICROSCOPY100
3.6695-3.83650.52391220.52123221ELECTRON MICROSCOPY100
3.8365-4.03880.59151370.49883157ELECTRON MICROSCOPY100
4.0388-4.29180.49641440.41873219ELECTRON MICROSCOPY100
4.2918-4.62320.34551440.31443188ELECTRON MICROSCOPY100
4.6232-5.08840.3321280.27393183ELECTRON MICROSCOPY100
5.0884-5.82450.35371330.25913177ELECTRON MICROSCOPY100
5.8245-7.33760.35331390.28133179ELECTRON MICROSCOPY99
7.3376-82.52580.18241340.15373198ELECTRON MICROSCOPY100
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

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)
12.3086-0.02331.31247.6064-2.25581.8513-1.22560.6622-2.4865-2.835-0.902-0.31963.67550.73543.24962.94770.34380.70232.56130.13832.1845-19.8685-59.694145.0171
26.4784-6.6834-0.81827.07712.06061.7805-4.6301-0.031-1.5712-1.9382-0.3008-4.75645.11642.42051.8542.90550.59240.12892.6520.14641.7945-27.8419-57.880552.5911
34.39983.9656-0.87415.5185-4.32974.36572.4535-0.78791.47790.41360.02490.5246-2.3876-2.5955-0.92472.239-0.46960.3592.72570.44272.0117-20.7276-42.477253.4378
43.51342.5952.00962.91650.48043.28023.3293.25145.7456-2.39760.4301-6.14380.5008-1.9099-1.5023.0885-0.21220.57262.37820.97924.4036-27.2746-37.650247.4926
55.08272.20366.93382.29862.89859.80982.75132.0373.5469-0.7635-1.5781-5.2305-3.2058-8.6076-1.53092.5837-0.73551.22563.5917-0.27263.9471-34.9596-44.94351.0881
63.8292-3.28092.44575.4054-1.48613.70240.77383.0887-2.6033-0.70090.00823.1519-0.4139-0.5333-0.28651.9470.12120.47113.25990.57052.6063-25.0297-49.666344.3259
73.13441.3175-0.20024.5288-4.16368.22170.55840.7544-1.27031.1092-1.8-3.8301-3.0723-2.43681.38512.65730.31680.39223.24150.31962.1953-13.6516-50.394651.4788
85.3181-0.4181-3.08253.2759-2.44545.2769-1.7892-2.2938-2.94951.65771.6739-2.25861.31814.61152.04422.8427-0.23620.56962.18070.34572.2741-17.7062-58.948558.0431
97.4519-2.90133.51585.86194.22548.7329-0.0210.04-1.12880.4999-0.12321.51191.5499-0.9868-0.24152.44670.0270.31071.69560.2591.7073-59.5276-57.011519.5543
106.3951-4.53954.52758.05960.79287.1198-5.36988.55521.7274-6.06451.66120.4691-4.12534.281-1.64662.97730.3540.54442.6351-0.434.2159-45.6116-57.517916.4966
114.67123.8948-0.50634.19810.86442.3780.4179-1.2071-0.7969-4.89992.43961.3197-3.68866.7144-1.61814.40530.96560.80992.79750.173.0913-48.7355-47.344119.9532
125.38773.1133-2.66673.23841.6634.2632-0.39483.78290.636-6.59330.7732-0.1195-4.53531.4559-0.57262.7375-0.62580.57371.98670.21482.5346-57.3656-54.16413.2973
133.84380.20173.16444.29553.24665.502-0.49350.762-0.93721.6224-0.45321.6291.4659-1.46370.85512.4745-0.21710.43172.54530.18132.0959-65.9519-60.298123.5971
145.3249-2.9741-3.57844.1198-0.04213.57291.05481.0054-1.9588-3.58450.1956-0.54543.9757-1.55410.98062.92170.13790.29222.80790.22062.3631-37.6389-70.384465.6097
157.3171-2.182-4.85672.44641.28313.984-2.00342.7902-4.1002-2.2401-0.9434-0.69691.6212.8939-0.18462.9313-0.1304-0.10241.35390.07242.1294-42.3413-63.717873.2774
163.4182-1.87681.50028.67590.67552.85780.1686-1.16472.0085-0.22551.0045-0.7468-1.45042.7613-0.46611.5396-0.05940.06292.29080.1181.8873-26.7653-57.036874.0874
174.01911.1004-1.23.4026-3.94294.81181.1616-0.25961.7076-7.18421.0756-6.3914-3.91-2.9004-1.72382.2804-1.47862.4242.54040.8454.1728-28.3989-49.099268.2094
187.7522-1.2718-4.71986.1774.71595.38084.153-0.93122.4559-4.21772.3088-6.7004-4.7786-0.6461-1.77972.67670.22350.52713.93860.78454.1184-39.0306-49.382771.7923
195.8322-2.50742.00676.36094.99117.220.11322.05460.9673-4.90633.06891.79-7.2556-0.2722-1.88882.77780.7110.64622.52470.38042.7588-37.3132-58.055566.7112
205.66022.5904-0.79721.1934-0.52344.5751-1.20762.78092.322-3.2099-0.6624-0.831-2.50734.20390.38173.47660.90340.95471.80630.35992.0494-27.8292-63.312360.4737
213.7586-1.5791-1.76872.2661-0.02364.10410.6119-0.6706-1.3107-3.5428-2.2104-0.8054-0.26633.69230.65692.80390.37560.35943.11360.22271.9789-26.829-67.638972.1522
228.8979-2.1098-0.714.11053.64435.212-1.50762.2526-1.1571-0.64641.76711.98651.16363.16010.47092.5429-0.13440.48052.07380.20772.3664-35.5573-71.259578.6755
232.50273.01472.64185.54264.64594.39382.40531.70045.6296-3.598-4.1739-2.0614-0.55461.93551.03792.92170.27640.27632.740.53222.7911-49.9632-14.003619.1473
244.8993-0.02273.86145.1078-0.73733.2687-1.62783.28495.9523-3.5581-6.7748-1.0959-0.23631.94634.15943.10540.36680.63971.44910.20411.0583-44.6617-20.264226.6861
254.3463.36760.62285.38564.00233.83010.0565-1.99031.9678-0.01560.48130.72873.00821.1114-1.75581.7347-0.19080.07962.4126-0.18681.7991-57.2525-28.057529.6309
263.25910.04492.94034.7135-0.15263.0481.42863.5279-0.4698-2.9335-2.24363.0343.89930.88390.34262.41380.00980.50823.05660.18792.1801-65.2543-28.697922.7159
277.28815.16155.28844.63164.09664.2519-0.37987.23491.5634-7.1087-2.43216.04730.01282.45151.40133.35760.6763-1.32213.5953-0.15364.9024-57.3807-36.104421.6148
286.59735.49563.44575.3641.22424.16181.99213.56514.7438-0.7086-1.96955.1649-0.23872.78720.96421.77840.27-0.32813.0140.36493.4618-46.8896-34.833625.1789
295.0435-2.15834.48335.4757-5.77337.2513.81734.45920.0102-5.65-1.8286-4.7745.15051.1909-0.99862.18970.5248-0.16822.45940.32222.9237-49.1879-26.381920.1747
304.5944-0.827-3.7692.20985.5585.19331.2245-0.4253-0.58010.826-1.41972.05021.4591-0.5930.98483.27150.31160.41212.7229-0.02132.0355-60.1424-18.798122.4705
316.1491-5.73221.36196.7052-0.52833.381-0.7573-2.34050.66452.15170.5431-1.2399-3.3858-1.71470.47832.69780.02260.01622.45780.04162.1138-52.0867-13.298732.1055
322.88161.0480.99932.48121.17571.4192-1.76394.2243-2.7549-1.4097-0.9509-4.21381.01960.62632.11732.2034-0.23230.52773.1327-0.02522.7829-13.7726-39.796924.2755
334.14352.86162.26856.08610.85211.3962-4.54091.6504-1.4018-1.9423-0.5121-7.10491.20373.52790.72181.6687-0.5811-0.07923.33330.061.0116-20.8712-43.862131.826
348.4799-1.3664-6.21752.40651.69215.20110.0317-1.3509-0.15012.42451.0145-0.6233-0.8222-4.0556-1.14672.2371-0.1657-0.19691.75720.21341.8712-26.3005-30.051234.7797
355.99145.66565.6896.70815.84415.6763-0.51883.9862.7285-1.7134-0.82830.48450.0641.7909-0.25322.9339-0.22230.11182.7191-0.11931.7813-25.4647-22.062227.8794
362.2796-6.5315.52917.81510.1183.48741.2687.38631.7085-1.25890.5682-2.30190.9438-2.1316-0.36923.5426-0.03860.36212.26051.24474.0323-34.2168-28.535626.8694
372.7121-3.2904-1.00924.47971.43670.4881-3.33762.84632.26791.75264.5377-1.12964.2123-3.0344-1.26424.7855-1.2190.36182.92871.33243.6801-34.8646-39.138430.4373
383.84990.51380.66724.0625-2.13393.14710.24234.6076-2.8633-2.24222.10954.53530.8305-6.6607-2.4462.769-0.74510.25042.96850.6123.4398-26.1046-38.318325.3511
394.5689-2.07923.85016.2379-1.69733.5227-2.29862.2445-0.0025-4.06232.35252.88830.49574.3875-0.83972.1568-0.3637-0.00143.20660.00172.1039-19.9992-29.350919.1209
403.0617-3.2209-0.39973.18641.56012.7819-0.5674-0.92921.09846.46570.2831-2.676-2.80971.05540.26922.9449-0.1588-0.10963.11550.27642.0143-15.5129-28.755630.7475
413.24470.7369-2.33352.7959-1.53443.24450.6425-1.7846-0.30550.6252-0.1219-2.3568-3.21154.21730.44812.820.21190.40772.57120.19292.157-12.6746-37.817237.2925
421.88511.73891.25681.87432.17891.9648-1.54231.2017-2.1327-5.6072-0.94761.93-2.02331.00652.43583.4594-0.08740.26291.7682-0.14232.1633-45.8073-70.599229.4734
436.8351-8.1002-5.36442.00966.42144.4429-0.70380.3676-3.446-1.8816-4.2615-0.9316-2.43343.79220.62483.1922-0.48930.11951.42150.73311.7484-48.4542-62.889337.0816
444.2452-0.5481-3.37034.45252.50534.5827-0.5147-0.542-2.21651.68731.6967-0.1408-3.13811.4562-1.24171.61310.08650.352.45310.55841.769-33.9068-60.102540.0054
454.17585.64741.33428.3151.30720.4055-2.43690.0044-0.44280.0379-1.759-8.25392.7639-0.61892.12182.91770.72950.01982.75860.02242.0516-26.2213-62.4133.0667
462.04233.15512.48114.4423-0.53071.0063.66250.1077-0.5037-4.66261.6185-3.7693-3.0172-2.381-2.0062.04450.26141.5973.30150.5234.1712-30.9839-52.64332.0416
476.8149-1.0371-0.8110.3232-0.46756.90673.17712.6243-0.9824-3.27753.4356-8.0883-3.38610.7425-1.77650.13922.49981.37634.3266-0.24574.5999-41.2705-50.00835.6006
485.1479-3.4807-2.9865.63757.03048.9455-0.53972.08043.1368-4.23511.03112.5864-7.44182.3563-0.68882.90610.21570.61161.75390.30712.6569-42.0418-58.789530.5325
497.0546-0.94035.66293.1781-1.69884.8307-0.91331.93042.2446-0.6540.725-1.78795.18930.54681.52522.89710.20710.75151.97440.35232.3333-34.3895-66.457924.3301
503.1092-1.6854-4.8192.61812.66039.6231-0.4277-4.1068-2.89721.37940.6762-0.8585-0.947-0.30010.9812.8355-0.32940.2083.12510.72652.2978-34.6455-70.924435.9103
513.89471.21362.17464.4544.06215.28742.1150.8268-2.19853.4624-0.78790.88383.69131.73240.40212.9034-0.21330.17052.89410.14562.2259-44.0774-72.011442.4237
523.39294.1769-2.6155.9702-4.66053.4282-0.96251.86840.5149-1.4982.1969-2.61512.30842.1427-0.19232.8469-0.21250.48652.81520.23332.1772-15.4844-31.877460.4511
530.4128-0.13890.72261.9007-3.77282.42980.29744.01842.36840.334-1.7971-8.11792.145-2.39322.14171.8821-0.70780.27063.0415-0.06791.7968-21.2462-37.655668.0522
546.2119-1.78575.28621.90962.73886.27443.12330.73260.72414.94540.3859-0.0673-1.3579-5.4277-1.20582.02880.61120.96861.99220.21042.174-30.266-25.917270.94
554.54640.1051.53096.8815-6.97656.68420.81510.60432.0521.30441.19423.69230.798-1.1107-2.15592.65850.17350.18722.33050.45072.4245-35.3508-22.983163.3777
562.86472.17040.02614.691-3.24675.0248-0.97642.3411-1.6439-3.66772.60190.58781.4673-3.7555-1.33392.7493-0.34410.35732.56210.75142.5904-30.2014-34.723863.0092
577.4103-2.67795.45392.4931-3.29314.7101-0.91611.54461.4428-0.0112-0.36750.7909-2.439-1.51270.90683.112-0.46470.09372.79690.41081.8759-21.283-22.167663.8233
583.9512.5028-0.01194.9457-2.14413.1431.15760.1713-2.19113.4-1.6554-2.0062-1.34030.00710.84272.1131-0.01570.09072.42310.39362.5669-15.0318-29.641773.4766
597.39535.38014.95936.31786.05295.8984-1.33942.5176-2.0938-1.09482.25121.45680.719-2.1728-0.88391.868-0.3219-0.02062.87880.31412.1054-71.4952-41.542470.8309
603.51-1.8199-2.74649.24327.00415.8675-0.49693.56261.15390.1237-2.26385.89880.7435-1.90020.12531.6122-0.20330.80823.11850.25222.6526-64.0742-38.202778.4298
618.34450.9855-2.83638.05363.63583.1372.1766-1.98520.54862.4976-0.2838-0.99343.90466.2346-0.34292.29870.91670.10711.36650.59891.8603-59.8296-52.382881.3345
627.39851.15485.84013.5482.26735.94321.43231.4699-2.5466-0.44070.1053-3.5648-0.1442.1663-2.10322.7536-0.20750.54172.22420.18172.6115-56.1101-56.950273.7703
637.75622.08465.6463.9264.77547.21760.20374.2095-8.55062.07880.6964-2.2796-4.10997.3453-0.77673.8393-0.92650.73312.5759-0.49953.9399-50.5718-44.142976.9263
645.93733.21225.31615.05851.83465.8393.05914.66942.7792-2.54280.7254-0.34431.23226.5203-0.59222.1391-0.51290.44572.1533-0.15882.5795-59.3564-44.189271.8773
651.9306-1.8126-0.97383.2934-2.55122.13290.30622.1021-5.13170.2919-2.7592-3.2313.06472.18382.78111.2698-0.61580.91863.2566-0.12212.0984-66.2886-52.527165.6794
663.98490.89443.95793.26863.72895.139-0.71370.48770.8335-0.23980.16910.97621.52090.10190.73692.4555-0.21480.3212.12940.17762.0014-71.6845-48.253880.4671
675.2844-2.39342.32515.29323.66456.7627-0.55981.7401-1.6889-1.0971.05913.2677-0.9741-1.37990.84032.2081-0.44170.24842.39220.00442.4624-64.1991-61.007650.1041
685.90175.29590.8754.8080.09812.4704-3.79910.1249-7.24690.10910.22953.72482.1331.20460.90782.4813-0.18740.23323.03480.1451.8939-60.955-53.482257.7039
697.5447-4.7817-5.72113.61713.92075.5124-2.85840.5472-1.64984.53223.05641.2471-2.75872.9123-0.27962.49820.58390.57511.60490.53182.0618-48.3437-61.317160.6681
705.6048-3.13542.7714.63031.06284.05581.06711.7606-2.1431.5721-3.1897-5.3498-0.85493.811-1.40242.85020.11060.03922.16580.37972.2285-44.3268-68.193453.7281
714.6116-4.4331.51416.29551.01825.98261.96411.0815-5.9587-5.24342.6056-4.9281-1.42920.2126-0.19342.16030.46231.06032.6001-0.36133.8891-41.1579-57.849552.745
722.1142-2.12817.87032.00832.01543.3549-1.88172.3143-10.5497-2.49014.68230.0399-7.45513.2051-1.22944.40320.64140.67422.8764-0.22073.3618-46.9094-48.954156.2986
735.0698-2.52520.73253.8122.67255.2184-0.45794.06273.0324-3.46772.93552.3253-3.86034.1084-1.75653.0342-0.30890.52381.96740.15423.4249-53.435-54.844751.2128
744.115-4.5472-2.70385.34813.41742.98470.00910.2405-0.2756-2.2758-0.1232-4.07712.083-0.3727-1.33353.7424-0.04170.79752.5168-0.05662.0249-52.9868-65.725744.994
752.11281.23432.10012.6922.27642.4264-0.33061.9685-2.33131.13830.22831.1698-0.88480.20681.85683.2016-0.26980.54122.6376-0.04631.9629-56.222-68.86456.6048
763.54123.82532.27916.84874.89954.33391.42171.3287-1.1580.9488-1.12571.69322.00290.47320.28952.29350.22240.39052.13510.17292.4112-63.9541-63.183863.1151
775.31540.1017-4.24743.58932.34435.4354-0.2032.06271.3746-2.4995-1.2258-3.18920.45473.0941.60882.2922-0.20390.40912.4660.52862.3587-29.233-16.339839.832
782.074910.01070.13221.87575.23624.23081.81511.27445.52730.6158-5.4067-2.02661.05171.0596-0.11212.5536-0.8090.40382.57760.31461.816-29.59-24.538847.4026
792.6507-1.2390.44383.20890.33448.5466-2.5925-1.6134-0.23081.69322.94771.0359-0.1833-2.7993-0.82482.38860.41450.15772.3873-0.02241.8841-46.0418-20.380548.238
805.8619-2.9612-1.24292.63932.87915.213-1.05930.21813.518-8.02420.87816.9711-4.7476-1.52060.03192.44530.4719-1.03053.29590.24254.8974-49.6057-27.651142.3341
811.94790.49910.3872.7933-2.85033.6356-3.2052-2.10734.80860.09461.41484.02136.8086-0.6983-0.18382.57260.65480.05393.30950.67813.7954-41.0113-33.876245.8973
825.3615-3.3713-3.98294.31990.112710.0019-0.37391.1751-2.9896-2.78121.2143-3.96021.3092-2.2182-0.85443.2329-0.1881-0.43551.3380.4322.8381-37.0143-25.981640.8796
832.2153-5.36680.43747.90310.85130.17161.04143.2172-1.2079-4.08630.56733.5688-6.49591.2819-0.65264.8892-0.0435-0.07592.37060.53691.7425-41.3372-15.996434.6634
846.7605-6.70415.12828.8344-6.45794.6315-2.6644-1.57413.45641.3175-2.4051-1.4405-2.8287-2.642.10863.25680.3134-0.05932.88740.15582.0468-39.5507-11.90946.3164
855.13553.1371-4.19454.3644-2.92065.062.15353.06021.02262.6855-0.8652-1.6664-4.8585-1.42320.32682.16770.05770.14282.93990.3272.2938-30.3559-14.404652.9233
864.60633.17514.32622.94733.09573.5777-2.46431.50842.3793-1.3152-0.28060.7585-2.42-0.31010.27972.29830.2288-0.02232.5170.4612.912-70.2078-33.518334.5896
872.6461-1.44341.09642.40111.37272.8423-0.85565.03781.3004-1.5558-0.6342.42680.0823-0.38111.11571.83710.49320.1142.98720.11231.7503-62.0795-32.321242.1949
884.6771.76012.68314.71584.54246.74422.5559-0.7535-1.69272.3191-2.384-1.18893.0613-1.09150.19672.4238-0.43360.17091.96620.40521.6565-63.2046-49.215843.1085
893.18191.31431.24485.79443.37652.3180.9339.3741-4.0796-1.97880.42041.67270.18583.0186-1.12083.82570.3798-0.23192.6528-0.93063.424-55.3336-51.479737.133
903.7276-3.16362.46383.4548-0.98352.67834.77430.1793-3.28110.946-2.8011.7671-2.64217.8221-2.15653.397-0.5797-0.27152.48920.23312.9411-50.8381-41.898140.672
919.3584.54436.78632.0103-7.19181.92590.3884.7256.0564-7.97992.441-0.91912.9865.8968-0.32531.0932-0.4360.19663.7255-0.67823.3217-59.2882-39.439935.6713
921.53953.0886-1.02822.0349-4.36621.418-0.8561.751-2.10742.7204-1.1727-1.23441.9635-4.80720.36042.2221-0.53010.58054.6591-0.63061.7118-68.3065-45.504529.4975
933.4160.0313-3.52573.29391.43684.9647-1.5351-1.46710.94780.8072-1.65413.95942.6047-1.33720.92872.9429-0.39930.58633.1481-0.16442.4934-72.6479-44.417841.1008
945.00121.42954.65723.50261.86686.0032.7454-3.09491.2702-3.3338-1.61411.46391.5825-1.6908-1.3512.635-0.10690.33192.4635-0.05352.1732-71.8594-34.902347.5921
956.6166-1.5314.16134.52562.87395.77162.26363.45372.8284-1.8076-1.59081.72711.35812.02030.54632.7309-0.0120.11012.36120.64832.3902-57.4833-17.216755.3169
965.3185-5.5236-0.3236.5781.10732.4995-1.3017-1.17293.6897-2.85890.99244.11441.89820.013-1.60912.33410.46930.24782.43550.12762.0929-50.6911-21.687762.862
974.0074.92771.48474.2992.11352.28681.60860.6976-1.467-0.99362.1935-0.14964.69-0.3186-2.15292.0048-0.25520.17112.27920.07911.9436-60.5399-32.746965.8515
983.8774-0.18172.68675.48355.24375.52842.33162.3503-3.4082-0.7737-0.94331.1140.8533-2.2416-2.56652.1711-0.12520.0782.32960.06952.4482-62.5533-38.311758.3113
992.03992.0643-2.1682.3448-2.222.40642.4604-0.66381.05911.3314-0.82757.19013.38883.0236-0.99183.2176-0.1792-0.20933.62390.21933.5703-48.6772-36.323861.4258
1002.9874-1.7098-0.33094.5081-4.56567.77560.23042.07742.1142-3.25780.5563-3.2251-0.5091-1.8738-1.10791.86720.414-0.10023.00170.142.8719-53.3071-28.882156.3591
1017.9089-2.05541.93346.15274.41415.0784-0.76830.4556-1.42020.68871.10581.415-1.8313-5.4829-1.92573.28241.1606-0.38764.00160.04512.1053-64.0691-27.336850.1699
1023.50521.39152.81462.6146-0.22552.62161.6566-0.64062.6654-1.015-2.26990.9046-0.3051-0.56120.46882.43390.11550.26013.01160.2171.8321-66.6298-23.641861.7652
1035.3615-4.00530.03015.96172.14183.2663-2.5942-1.34551.6834-1.84881.338-1.31482.0871-2.27840.84922.3353-0.23080.01582.45390.11792.3994-59.7195-17.079868.3035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain 'G' and (resid 1 through 11 )
2ELECTRON MICROSCOPY2chain 'G' and (resid 12 through 16 )
3ELECTRON MICROSCOPY3chain 'G' and (resid 17 through 34 )
4ELECTRON MICROSCOPY4chain 'G' and (resid 35 through 41 )
5ELECTRON MICROSCOPY5chain 'G' and (resid 42 through 46 )
6ELECTRON MICROSCOPY6chain 'G' and (resid 47 through 63 )
7ELECTRON MICROSCOPY7chain 'G' and (resid 64 through 75 )
8ELECTRON MICROSCOPY8chain 'G' and (resid 76 through 85 )
9ELECTRON MICROSCOPY9chain 'L' and (resid 1 through 34 )
10ELECTRON MICROSCOPY10chain 'L' and (resid 35 through 41 )
11ELECTRON MICROSCOPY11chain 'L' and (resid 42 through 46 )
12ELECTRON MICROSCOPY12chain 'L' and (resid 47 through 63 )
13ELECTRON MICROSCOPY13chain 'L' and (resid 64 through 85 )
14ELECTRON MICROSCOPY14chain 'K' and (resid 1 through 11 )
15ELECTRON MICROSCOPY15chain 'K' and (resid 12 through 16 )
16ELECTRON MICROSCOPY16chain 'K' and (resid 17 through 34 )
17ELECTRON MICROSCOPY17chain 'K' and (resid 35 through 41 )
18ELECTRON MICROSCOPY18chain 'K' and (resid 42 through 46 )
19ELECTRON MICROSCOPY19chain 'K' and (resid 47 through 58 )
20ELECTRON MICROSCOPY20chain 'K' and (resid 59 through 63 )
21ELECTRON MICROSCOPY21chain 'K' and (resid 64 through 75 )
22ELECTRON MICROSCOPY22chain 'K' and (resid 76 through 85 )
23ELECTRON MICROSCOPY23chain 'J' and (resid 1 through 11 )
24ELECTRON MICROSCOPY24chain 'J' and (resid 12 through 16 )
25ELECTRON MICROSCOPY25chain 'J' and (resid 17 through 29 )
26ELECTRON MICROSCOPY26chain 'J' and (resid 30 through 34 )
27ELECTRON MICROSCOPY27chain 'J' and (resid 35 through 41 )
28ELECTRON MICROSCOPY28chain 'J' and (resid 42 through 46 )
29ELECTRON MICROSCOPY29chain 'J' and (resid 47 through 58 )
30ELECTRON MICROSCOPY30chain 'J' and (resid 59 through 75 )
31ELECTRON MICROSCOPY31chain 'J' and (resid 76 through 85 )
32ELECTRON MICROSCOPY32chain 'I' and (resid 1 through 11 )
33ELECTRON MICROSCOPY33chain 'I' and (resid 12 through 16 )
34ELECTRON MICROSCOPY34chain 'I' and (resid 17 through 29 )
35ELECTRON MICROSCOPY35chain 'I' and (resid 30 through 34 )
36ELECTRON MICROSCOPY36chain 'I' and (resid 35 through 41 )
37ELECTRON MICROSCOPY37chain 'I' and (resid 42 through 46 )
38ELECTRON MICROSCOPY38chain 'I' and (resid 47 through 58 )
39ELECTRON MICROSCOPY39chain 'I' and (resid 59 through 63 )
40ELECTRON MICROSCOPY40chain 'I' and (resid 64 through 75 )
41ELECTRON MICROSCOPY41chain 'I' and (resid 76 through 85 )
42ELECTRON MICROSCOPY42chain 'H' and (resid 1 through 11 )
43ELECTRON MICROSCOPY43chain 'H' and (resid 12 through 16 )
44ELECTRON MICROSCOPY44chain 'H' and (resid 17 through 29 )
45ELECTRON MICROSCOPY45chain 'H' and (resid 30 through 34 )
46ELECTRON MICROSCOPY46chain 'H' and (resid 35 through 41 )
47ELECTRON MICROSCOPY47chain 'H' and (resid 42 through 46 )
48ELECTRON MICROSCOPY48chain 'H' and (resid 47 through 58 )
49ELECTRON MICROSCOPY49chain 'H' and (resid 59 through 63 )
50ELECTRON MICROSCOPY50chain 'H' and (resid 64 through 75 )
51ELECTRON MICROSCOPY51chain 'H' and (resid 76 through 85 )
52ELECTRON MICROSCOPY52chain 'F' and (resid 1 through 11 )
53ELECTRON MICROSCOPY53chain 'F' and (resid 12 through 16 )
54ELECTRON MICROSCOPY54chain 'F' and (resid 17 through 29 )
55ELECTRON MICROSCOPY55chain 'F' and (resid 30 through 41 )
56ELECTRON MICROSCOPY56chain 'F' and (resid 42 through 58 )
57ELECTRON MICROSCOPY57chain 'F' and (resid 59 through 75 )
58ELECTRON MICROSCOPY58chain 'F' and (resid 76 through 85 )
59ELECTRON MICROSCOPY59chain 'E' and (resid 1 through 11 )
60ELECTRON MICROSCOPY60chain 'E' and (resid 12 through 16 )
61ELECTRON MICROSCOPY61chain 'E' and (resid 17 through 29 )
62ELECTRON MICROSCOPY62chain 'E' and (resid 30 through 41 )
63ELECTRON MICROSCOPY63chain 'E' and (resid 42 through 46 )
64ELECTRON MICROSCOPY64chain 'E' and (resid 47 through 58 )
65ELECTRON MICROSCOPY65chain 'E' and (resid 59 through 63 )
66ELECTRON MICROSCOPY66chain 'E' and (resid 64 through 85 )
67ELECTRON MICROSCOPY67chain 'D' and (resid 1 through 11 )
68ELECTRON MICROSCOPY68chain 'D' and (resid 12 through 16 )
69ELECTRON MICROSCOPY69chain 'D' and (resid 17 through 29 )
70ELECTRON MICROSCOPY70chain 'D' and (resid 30 through 34 )
71ELECTRON MICROSCOPY71chain 'D' and (resid 35 through 41 )
72ELECTRON MICROSCOPY72chain 'D' and (resid 42 through 46 )
73ELECTRON MICROSCOPY73chain 'D' and (resid 47 through 58 )
74ELECTRON MICROSCOPY74chain 'D' and (resid 59 through 63 )
75ELECTRON MICROSCOPY75chain 'D' and (resid 64 through 75 )
76ELECTRON MICROSCOPY76chain 'D' and (resid 76 through 85 )
77ELECTRON MICROSCOPY77chain 'C' and (resid 1 through 11 )
78ELECTRON MICROSCOPY78chain 'C' and (resid 12 through 16 )
79ELECTRON MICROSCOPY79chain 'C' and (resid 17 through 34 )
80ELECTRON MICROSCOPY80chain 'C' and (resid 35 through 41 )
81ELECTRON MICROSCOPY81chain 'C' and (resid 42 through 46 )
82ELECTRON MICROSCOPY82chain 'C' and (resid 47 through 58 )
83ELECTRON MICROSCOPY83chain 'C' and (resid 59 through 63 )
84ELECTRON MICROSCOPY84chain 'C' and (resid 64 through 75 )
85ELECTRON MICROSCOPY85chain 'C' and (resid 76 through 85 )
86ELECTRON MICROSCOPY86chain 'B' and (resid 1 through 11 )
87ELECTRON MICROSCOPY87chain 'B' and (resid 12 through 16 )
88ELECTRON MICROSCOPY88chain 'B' and (resid 17 through 34 )
89ELECTRON MICROSCOPY89chain 'B' and (resid 35 through 41 )
90ELECTRON MICROSCOPY90chain 'B' and (resid 42 through 46 )
91ELECTRON MICROSCOPY91chain 'B' and (resid 47 through 58 )
92ELECTRON MICROSCOPY92chain 'B' and (resid 59 through 63 )
93ELECTRON MICROSCOPY93chain 'B' and (resid 64 through 75 )
94ELECTRON MICROSCOPY94chain 'B' and (resid 76 through 85 )
95ELECTRON MICROSCOPY95chain 'A' and (resid 1 through 11 )
96ELECTRON MICROSCOPY96chain 'A' and (resid 12 through 16 )
97ELECTRON MICROSCOPY97chain 'A' and (resid 17 through 29 )
98ELECTRON MICROSCOPY98chain 'A' and (resid 30 through 41 )
99ELECTRON MICROSCOPY99chain 'A' and (resid 42 through 46 )
100ELECTRON MICROSCOPY100chain 'A' and (resid 47 through 58 )
101ELECTRON MICROSCOPY101chain 'A' and (resid 59 through 63 )
102ELECTRON MICROSCOPY102chain 'A' and (resid 64 through 75 )
103ELECTRON MICROSCOPY103chain 'A' and (resid 76 through 85 )

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  • 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

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