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- PDB-8yd8: Structure of FADD/Caspase-8/cFLIP death effector domain assembly -

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Basic information

Entry
Database: PDB / ID: 8yd8
TitleStructure of FADD/Caspase-8/cFLIP death effector domain assembly
Components
  • CASP8 and FADD-like apoptosis regulator subunit p43
  • Caspase-8Caspase 8
  • FAS-associated death domain protein
KeywordsAPOPTOSIS / FADD / Caspase-8 / cFLIP / death effector domain
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of myoblast fusion / negative regulation of activation-induced cell death of T cells / skeletal myofibril assembly / caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / skeletal muscle atrophy / tumor necrosis factor receptor superfamily binding ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of myoblast fusion / negative regulation of activation-induced cell death of T cells / skeletal myofibril assembly / caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / skeletal muscle atrophy / tumor necrosis factor receptor superfamily binding / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / death-inducing signaling complex assembly / TRAIL-activated apoptotic signaling pathway / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of necroptotic process / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / skeletal muscle tissue regeneration / positive regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / positive regulation of macrophage differentiation / caspase binding / necroptotic signaling pathway / self proteolysis / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / negative regulation of hepatocyte apoptotic process / natural killer cell activation / CLEC7A/inflammasome pathway / receptor serine/threonine kinase binding / negative regulation of necroptotic process / activation of cysteine-type endopeptidase activity / positive regulation of innate immune response / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of hepatocyte proliferation / positive regulation of extrinsic apoptotic signaling pathway / cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cellular response to transforming growth factor beta stimulus / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / negative regulation of cardiac muscle cell apoptotic process / execution phase of apoptosis / RIPK1-mediated regulated necrosis / positive regulation of execution phase of apoptosis / response to testosterone / B cell activation / regulation of innate immune response / positive regulation of activated T cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / T cell homeostasis / behavioral response to cocaine / positive regulation of proteolysis / macrophage differentiation / protein maturation / cellular response to organic cyclic compound / extrinsic apoptotic signaling pathway via death domain receptors / cellular response to nitric oxide / Caspase-mediated cleavage of cytoskeletal proteins / lymph node development / response to tumor necrosis factor / enzyme activator activity / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / skeletal muscle tissue development / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of reactive oxygen species biosynthetic process / keratinocyte differentiation / cysteine-type peptidase activity / extrinsic apoptotic signaling pathway in absence of ligand / regulation of cytokine production / spleen development / cellular response to epidermal growth factor stimulus / T cell activation / cellular response to dexamethasone stimulus / erythrocyte differentiation / proteolysis involved in protein catabolic process / thymus development / kidney development / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / cellular response to estradiol stimulus / positive regulation of interleukin-8 production
Similarity search - Function
: / FADD / Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...: / FADD / Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
CASP8 and FADD-like apoptosis regulator / FAS-associated death domain protein / Caspase-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsLin, S.-C. / Yang, C.-Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Other government Taiwan
CitationJournal: Nat Commun / Year: 2024
Title: Deciphering DED assembly mechanisms in FADD-procaspase-8-cFLIP complexes regulating apoptosis.
Authors: Chao-Yu Yang / Chia-I Lien / Yi-Chun Tseng / Yi-Fan Tu / Arkadiusz W Kulczyk / Yen-Chen Lu / Yin-Ting Wang / Tsung-Wei Su / Li-Chung Hsu / Yu-Chih Lo / Su-Chang Lin /
Abstract: Fas-associated protein with death domain (FADD), procaspase-8, and cellular FLICE-inhibitory proteins (cFLIP) assemble through death-effector domains (DEDs), directing death receptor signaling ...Fas-associated protein with death domain (FADD), procaspase-8, and cellular FLICE-inhibitory proteins (cFLIP) assemble through death-effector domains (DEDs), directing death receptor signaling towards cell survival or apoptosis. Understanding their three-dimensional regulatory mechanism has been limited by the absence of atomic coordinates for their ternary DED complex. By employing X-ray crystallography and cryogenic electron microscopy (cryo-EM), we present the atomic coordinates of human FADD-procaspase-8-cFLIP complexes, revealing structural insights into these critical interactions. These structures illustrate how FADD and cFLIP orchestrate the assembly of caspase-8-containing complexes and offer mechanistic explanations for their role in promoting or inhibiting apoptotic and necroptotic signaling. A helical procaspase-8-cFLIP hetero-double layer in the complex appears to promote limited caspase-8 activation for cell survival. Our structure-guided mutagenesis supports the role of the triple-FADD complex in caspase-8 activation and in regulating receptor-interacting protein kinase 1 (RIPK1). These results propose a unified mechanism for DED assembly and procaspase-8 activation in the regulation of apoptotic and necroptotic signaling across various cellular pathways involved in development, innate immunity, and disease.
History
DepositionFeb 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: CASP8 and FADD-like apoptosis regulator subunit p43
D: Caspase-8
C: Caspase-8
B: Caspase-8
E: Caspase-8
H: CASP8 and FADD-like apoptosis regulator subunit p43
J: CASP8 and FADD-like apoptosis regulator subunit p43
K: CASP8 and FADD-like apoptosis regulator subunit p43
L: FAS-associated death domain protein
A: Caspase-8


Theoretical massNumber of molelcules
Total (without water)217,54710
Polymers217,54710
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.170, 149.680, 175.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 4 or resid 6...
d_2ens_1(chain "B" and (resid 3 through 4 or resid 6...
d_3ens_1(chain "C" and (resid 3 through 4 or resid 6...
d_4ens_1(chain "D" and (resid 3 through 4 or resid 6...
d_5ens_1(chain "E" and (resid 3 through 4 or resid 6...
d_1ens_2(chain "H" and (resid 3 or resid 5 through 10...
d_2ens_2(chain "I" and (resid 3 or resid 5 through 10...
d_3ens_2(chain "J" and (resid 3 or resid 5 through 10...
d_4ens_2(chain "K" and (resid 3 or resid 5 through 10...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PHEPHESERSERAJ3 - 43 - 4
d_12ens_1ASNASNLEULEUAJ6 - 426 - 42
d_13ens_1LEULEUGLUGLUAJ44 - 5544 - 55
d_14ens_1SERSERTHRTHRAJ57 - 8157 - 81
d_15ens_1LYSLYSGLUGLUAJ83 - 8783 - 87
d_16ens_1GLUGLUGLYGLYAJ89 - 9489 - 94
d_17ens_1ALAALALEULEUAJ96 - 11796 - 117
d_18ens_1SERSERPHEPHEAJ119 - 120119 - 120
d_19ens_1GLYGLYGLNGLNAJ122 - 125122 - 125
d_110ens_1ILEILESERSERAJ128 - 129128 - 129
d_111ens_1CYSCYSASPASPAJ131 - 135131 - 135
d_112ens_1METMETGLYGLYAJ137 - 155137 - 155
d_113ens_1LEULEULYSLYSAJ157 - 161157 - 161
d_114ens_1VALVALALAALAAJ163 - 165163 - 165
d_115ens_1ILEILELEULEUAJ167 - 172167 - 172
d_116ens_1ILEILEGLUGLUAJ174 - 180174 - 180
d_21ens_1PHEPHESERSERBD3 - 43 - 4
d_22ens_1ASNASNLEULEUBD6 - 426 - 42
d_23ens_1LEULEUGLUGLUBD44 - 5544 - 55
d_24ens_1SERSERTHRTHRBD57 - 8157 - 81
d_25ens_1LYSLYSGLUGLUBD83 - 8783 - 87
d_26ens_1GLUGLUGLYGLYBD89 - 9489 - 94
d_27ens_1ALAALALEULEUBD96 - 11796 - 117
d_28ens_1SERSERPHEPHEBD119 - 120119 - 120
d_29ens_1GLYGLYGLNGLNBD122 - 125122 - 125
d_210ens_1ILEILESERSERBD128 - 129128 - 129
d_211ens_1CYSCYSASPASPBD131 - 135131 - 135
d_212ens_1METMETGLYGLYBD137 - 155137 - 155
d_213ens_1LEULEULYSLYSBD157 - 161157 - 161
d_214ens_1VALVALALAALABD163 - 165163 - 165
d_215ens_1ILEILELEULEUBD167 - 172167 - 172
d_216ens_1ILEILEGLUGLUBD174 - 180174 - 180
d_31ens_1PHEPHESERSERCC3 - 43 - 4
d_32ens_1ASNASNLEULEUCC6 - 426 - 42
d_33ens_1LEULEUGLUGLUCC44 - 5544 - 55
d_34ens_1SERSERTHRTHRCC57 - 8157 - 81
d_35ens_1LYSLYSGLUGLUCC83 - 8783 - 87
d_36ens_1GLUGLUGLYGLYCC89 - 9489 - 94
d_37ens_1ALAALALEULEUCC96 - 11796 - 117
d_38ens_1SERSERPHEPHECC119 - 120119 - 120
d_39ens_1GLYGLYGLNGLNCC122 - 125122 - 125
d_310ens_1ILEILESERSERCC128 - 129128 - 129
d_311ens_1CYSCYSASPASPCC131 - 135131 - 135
d_312ens_1METMETGLYGLYCC137 - 155137 - 155
d_313ens_1LEULEULYSLYSCC157 - 161157 - 161
d_314ens_1VALVALALAALACC163 - 165163 - 165
d_315ens_1ILEILELEULEUCC167 - 172167 - 172
d_316ens_1ILEILEGLUGLUCC174 - 180174 - 180
d_41ens_1PHEPHESERSERDB3 - 43 - 4
d_42ens_1ASNASNLEULEUDB6 - 426 - 42
d_43ens_1LEULEUGLUGLUDB44 - 5544 - 55
d_44ens_1SERSERTHRTHRDB57 - 8157 - 81
d_45ens_1LYSLYSGLUGLUDB83 - 8783 - 87
d_46ens_1GLUGLUGLYGLYDB89 - 9489 - 94
d_47ens_1ALAALALEULEUDB96 - 11796 - 117
d_48ens_1SERSERPHEPHEDB119 - 120119 - 120
d_49ens_1GLYGLYGLNGLNDB122 - 125122 - 125
d_410ens_1ILEILESERSERDB128 - 129128 - 129
d_411ens_1CYSCYSASPASPDB131 - 135131 - 135
d_412ens_1METMETGLYGLYDB137 - 155137 - 155
d_413ens_1LEULEULYSLYSDB157 - 161157 - 161
d_414ens_1VALVALALAALADB163 - 165163 - 165
d_415ens_1ILEILELEULEUDB167 - 172167 - 172
d_416ens_1ILEILEGLUGLUDB174 - 180174 - 180
d_51ens_1PHEPHESERSEREE3 - 43 - 4
d_52ens_1ASNASNLEULEUEE6 - 426 - 42
d_53ens_1LEULEUGLUGLUEE44 - 5544 - 55
d_54ens_1SERSERTHRTHREE57 - 8157 - 81
d_55ens_1LYSLYSGLUGLUEE83 - 8783 - 87
d_56ens_1GLUGLUGLYGLYEE89 - 9489 - 94
d_57ens_1ALAALALEULEUEE96 - 11796 - 117
d_58ens_1SERSERPHEPHEEE119 - 120119 - 120
d_59ens_1GLYGLYGLNGLNEE122 - 125122 - 125
d_510ens_1ILEILESERSEREE128 - 129128 - 129
d_511ens_1CYSCYSASPASPEE131 - 135131 - 135
d_512ens_1METMETGLYGLYEE137 - 155137 - 155
d_513ens_1LEULEULYSLYSEE157 - 161157 - 161
d_514ens_1VALVALALAALAEE163 - 165163 - 165
d_515ens_1ILEILELEULEUEE167 - 172167 - 172
d_516ens_1ILEILEGLUGLUEE174 - 180174 - 180
d_11ens_2ALAALAALAALAHF33
d_12ens_2VALVALGLUGLUHF5 - 105 - 10
d_13ens_2ALAALALEULEUHF12 - 4412 - 44
d_14ens_2GLUGLUVALVALHF46 - 6246 - 62
d_15ens_2ARGARGLEULEUHF64 - 8464 - 84
d_16ens_2ASNASNASPASPHF86 - 10586 - 105
d_17ens_2SERSERMETMETHF107 - 120107 - 120
d_18ens_2LYSLYSGLUGLUHF129 - 153129 - 153
d_19ens_2CYSCYSLYSLYSHF155 - 172155 - 172
d_110ens_2SERSERVALVALHF174 - 175174 - 175
d_21ens_2ALAALAALAALAIA33
d_22ens_2VALVALGLUGLUIA5 - 105 - 10
d_23ens_2ALAALAVALVALIA12 - 2812 - 28
d_24ens_2ASPASPLEULEUIA31 - 4431 - 44
d_25ens_2GLUGLUVALVALIA46 - 6246 - 62
d_26ens_2ARGARGLEULEUIA64 - 8464 - 84
d_27ens_2ASNASNASPASPIA86 - 10586 - 105
d_28ens_2SERSERMETMETIA107 - 120107 - 120
d_29ens_2LYSLYSGLUGLUIA129 - 153129 - 153
d_210ens_2CYSCYSLYSLYSIA155 - 172155 - 172
d_211ens_2SERSERVALVALIA174 - 175174 - 175
d_31ens_2ALAALAALAALAJG33
d_32ens_2VALVALGLUGLUJG5 - 105 - 10
d_33ens_2ALAALAVALVALJG12 - 2812 - 28
d_34ens_2ASPASPLEULEUJG31 - 4431 - 44
d_35ens_2GLUGLUVALVALJG46 - 6246 - 62
d_36ens_2ARGARGLEULEUJG64 - 8464 - 84
d_37ens_2ASNASNASPASPJG86 - 10586 - 105
d_38ens_2SERSERMETMETJG107 - 120107 - 120
d_39ens_2LYSLYSGLUGLUJG129 - 153129 - 153
d_310ens_2CYSCYSLYSLYSJG155 - 172155 - 172
d_311ens_2SERSERVALVALJG174 - 175174 - 175
d_41ens_2ALAALAALAALAKH33
d_42ens_2VALVALGLUGLUKH5 - 105 - 10
d_43ens_2ALAALAVALVALKH12 - 2812 - 28
d_44ens_2ASPASPLEULEUKH31 - 4431 - 44
d_45ens_2GLUGLUVALVALKH46 - 6246 - 62
d_46ens_2ARGARGLEULEUKH64 - 8464 - 84
d_47ens_2ASNASNASPASPKH86 - 10586 - 105
d_48ens_2SERSERMETMETKH107 - 120107 - 120
d_49ens_2LYSLYSGLUGLUKH129 - 153129 - 153
d_410ens_2CYSCYSLYSLYSKH155 - 172155 - 172
d_411ens_2SERSERVALVALKH174 - 175174 - 175

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.306588114495, 0.3953341365, -0.865860640385), (-0.315222245977, 0.900506683202, 0.299537391906), (0.898130649567, 0.181103931561, 0.400702760512)34.7063549643, 33.0468144142, -51.0381087319
2given(-0.806289671266, 0.312747084656, -0.502081892771), (-0.139741910565, 0.724062830556, 0.675429652768), (0.574777491244, 0.61475383565, -0.540100506492)102.891520985, 39.3154015892, -35.9317655367
3given(-0.808235900289, -0.143056873576, 0.571217524597), (0.332987381951, 0.689020931215, 0.643715433875), (-0.485668748167, 0.710482151268, -0.509255318856)113.168515699, 24.6749964766, 28.4239090047
4given(0.365316842106, -0.410042710444, 0.835708430306), (0.488990636668, 0.848449146553, 0.202539386204), (-0.792105903352, 0.334662548434, 0.510459808947)52.2735550411, 24.0596626313, 57.0061318969
5given(-0.567725306933, 0.355685152986, -0.742412316582), (-0.264193274682, 0.775415642663, 0.573526367944), (0.779672937507, 0.521745774357, -0.346253458408)87.8618693118, 21.247928038, -55.8793151479
6given(-0.963745414241, -0.00388513340765, 0.266795206606), (0.191545824479, 0.686024781481, 0.701911815201), (-0.185755144354, 0.727567800918, -0.660409056126)118.563144121, 8.53524237681, 0.372829629122
7given(-0.076549268222, -0.326345057711, 0.942146014608), (0.475161956585, 0.818777217827, 0.322218842686), (-0.87656221944, 0.472337560305, 0.0923899592822)73.6525455187, 1.61372436107, 51.5893820045

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Components

#1: Protein
CASP8 and FADD-like apoptosis regulator subunit p43 / cFLIP


Mass: 20797.385 Da / Num. of mol.: 4 / Mutation: H7G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFLAR, CASH, CASP8AP1, CLARP, MRIT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15519
#2: Protein
Caspase-8 / Caspase 8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH


Mass: 22011.449 Da / Num. of mol.: 5 / Mutation: F122G, L123G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, MCH5 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q14790, caspase-8
#3: Protein FAS-associated death domain protein / FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of ...FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of receptor induced toxicity


Mass: 24300.438 Da / Num. of mol.: 1 / Mutation: H9G
Source method: isolated from a genetically manipulated source
Details: FADD / Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q13158

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: HEPES, PEG 8000, TBG, TCEP, sodium chloride / PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.1→30.09 Å / Num. obs: 53985 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 102.95 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.215.60.91751850.790.940.4231.0120.81897.5
3.21-3.346.20.753540.8750.9660.3060.7660.85899.9
3.34-3.496.30.45953360.9490.9870.1990.5010.934100
3.49-3.676.30.28553540.9760.9940.1240.3120.991100
3.67-3.96.30.18353820.9890.9970.080.21.06799.9
3.9-4.216.20.10853680.9950.9990.0470.1181.0699.9
4.21-4.636.20.08153960.9960.9990.0360.0891.07699.9
4.63-5.296.20.06854380.9970.9990.030.0741.08699.9
5.29-6.666.20.06354910.9970.9990.0270.0691.059100
6.66-30.095.80.04256810.99810.0190.0461.01899.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→30.09 Å / SU ML: 0.4226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 2623 4.89 %5
Rwork0.1995 51054 --
obs0.2015 53677 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.02 Å2
Refinement stepCycle: LAST / Resolution: 3.11→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13754 0 0 0 13754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001713893
X-RAY DIFFRACTIONf_angle_d0.434818597
X-RAY DIFFRACTIONf_chiral_restr0.03632143
X-RAY DIFFRACTIONf_plane_restr0.00342376
X-RAY DIFFRACTIONf_dihedral_angle_d3.37051836
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JAX-RAY DIFFRACTIONTorsion NCS0.737379054013
ens_1d_3JAX-RAY DIFFRACTIONTorsion NCS0.800085098377
ens_1d_4JAX-RAY DIFFRACTIONTorsion NCS0.825031643248
ens_1d_5JAX-RAY DIFFRACTIONTorsion NCS0.963509025342
ens_2d_2FHX-RAY DIFFRACTIONTorsion NCS1.06345820494
ens_2d_3FHX-RAY DIFFRACTIONTorsion NCS0.92496759055
ens_2d_4FHX-RAY DIFFRACTIONTorsion NCS0.99539910409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.170.44071210.35112361X-RAY DIFFRACTION87.86
3.17-3.230.36561420.31842620X-RAY DIFFRACTION98.68
3.23-3.290.31241470.28282661X-RAY DIFFRACTION98.94
3.29-3.360.3731430.28782640X-RAY DIFFRACTION98.97
3.36-3.440.32331370.2782688X-RAY DIFFRACTION99.19
3.44-3.530.3811600.26232634X-RAY DIFFRACTION99.25
3.53-3.620.29641180.24612688X-RAY DIFFRACTION99.4
3.62-3.730.26761550.23372675X-RAY DIFFRACTION99.4
3.73-3.850.30731230.22082665X-RAY DIFFRACTION99.43
3.85-3.990.23961480.20822689X-RAY DIFFRACTION99.72
3.99-4.150.23791300.19482712X-RAY DIFFRACTION99.54
4.15-4.340.27381280.19312693X-RAY DIFFRACTION99.89
4.34-4.560.23111340.17912723X-RAY DIFFRACTION99.9
4.56-4.850.22411360.18452716X-RAY DIFFRACTION99.76
4.85-5.220.23611270.18962743X-RAY DIFFRACTION99.86
5.22-5.740.27331300.20932719X-RAY DIFFRACTION99.75
5.74-6.570.29341380.22042769X-RAY DIFFRACTION99.97
6.57-8.240.22241460.19292791X-RAY DIFFRACTION100
8.24-30.090.15021600.14372867X-RAY DIFFRACTION99.18

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