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- PDB-8cmf: Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV... -

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Basic information

Entry
Database: PDB / ID: 8cmf
TitleHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp3 epitope (orf1ab)1350-1364
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
  • SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
KeywordsIMMUNE SYSTEM / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen / major histocompatibility complex / major histocompatibility complex class 2 / SARS-CoV-2 / coronavirus / COVID-19 / nsp3 / orf1ab
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / early endosome membrane / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / adaptive immune response / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / immune response / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / Golgi membrane / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication
Similarity search - Function
MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus
Similarity search - Domain/homology
SUCCINIC ACID / HLA class II histocompatibility antigen, DR alpha chain / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMacLachlan, B.J. / Mason, G.H. / Sourfield, D.O. / Godkin, A.J. / Rizkallah, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Authors: Chen, Y. / Mason, G.H. / Scourfield, D.O. / Greenshields-Watson, A. / Haigh, T.A. / Sewell, A.K. / Long, H.M. / Gallimore, A.M. / Rizkallah, P. / MacLachlan, B.J. / Godkin, A.
History
DepositionFeb 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,45712
Polymers90,9736
Non-polymers4846
Water3,531196
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6665
Polymers45,4863
Non-polymers1802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7917
Polymers45,4863
Non-polymers3044
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.230, 95.490, 202.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 49 or resid 51...
d_2ens_1(chain "D" and (resid 2 through 49 or resid 51...
d_1ens_2(chain "B" and (resid 2 through 47 or resid 49...
d_2ens_2(chain "E" and (resid 2 through 47 or resid 49...
d_1ens_3chain "C"
d_2ens_3chain "F"

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_1LYSLYSGLYGLYAA2 - 493 - 50
d_12ens_1PHEPHEALAALAAA51 - 5652 - 57
d_13ens_1GLYGLYTHRTHRAA58 - 7459 - 75
d_14ens_1ARGARGVALVALAA76 - 8977 - 90
d_15ens_1VALVALLEULEUAA91 - 9992 - 100
d_16ens_1PROPROCYSCYSAA102 - 107103 - 108
d_17ens_1ILEILEPHEPHEAA109 - 145110 - 146
d_18ens_1LYSLYSPHEPHEAA147 - 180148 - 181
d_21ens_1LYSLYSGLYGLYDD2 - 493 - 50
d_22ens_1PHEPHEALAALADD51 - 5652 - 57
d_23ens_1GLYGLYTHRTHRDD58 - 7459 - 75
d_24ens_1ARGARGVALVALDD76 - 8977 - 90
d_25ens_1VALVALLEULEUDD91 - 9992 - 100
d_26ens_1PROPROCYSCYSDD102 - 107103 - 108
d_27ens_1ILEILEPHEPHEDD109 - 145110 - 146
d_28ens_1LYSLYSPHEPHEDD147 - 180148 - 181
d_11ens_2ASPASPTYRTYRBB2 - 476 - 51
d_12ens_2ALAALATHRTHRBB49 - 5153 - 55
d_13ens_2LEULEUALAALABB53 - 5857 - 62
d_14ens_2TYRTYRGLNGLNBB60 - 6464 - 68
d_15ens_2ASPASPGLUGLUBB66 - 6970 - 73
d_16ens_2ARGARGVALVALBB71 - 9175 - 95
d_17ens_2ARGARGSERSERBB93 - 10497 - 108
d_18ens_2THRTHRGLNGLNBB106 - 110110 - 114
d_19ens_2HISHISPROPROBB112 - 165116 - 169
d_110ens_2SERSERALAALABB167 - 190171 - 194
d_21ens_2ASPASPTYRTYREE2 - 476 - 51
d_22ens_2ALAALATHRTHREE49 - 5153 - 55
d_23ens_2LEULEUALAALAEE53 - 5857 - 62
d_24ens_2TYRTYRGLNGLNEE60 - 6464 - 68
d_25ens_2ASPASPGLUGLUEE66 - 6970 - 73
d_26ens_2ARGARGVALVALEE71 - 9175 - 95
d_27ens_2ARGARGSERSEREE93 - 10497 - 108
d_28ens_2THRTHRGLNGLNEE106 - 110110 - 114
d_29ens_2HISHISPROPROEE112 - 165116 - 169
d_210ens_2SERSERALAALAEE167 - 190171 - 194
d_11ens_3LYSLYSLYSLYSCC1 - 151 - 15
d_21ens_3LYSLYSLYSLYSFF1 - 151 - 15

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.990036658124, -0.136488704812, -0.0346157338473), (-0.0808432766885, 0.349688000797, 0.933371665904), (-0.115289983022, 0.926870614248, -0.357238133823)-27.9676943071, -41.3560611602, 54.9510774736
2given(-0.992846776376, -0.11375269969, -0.0362712276122), (-0.0721860233779, 0.329922590404, 0.941243997256), (-0.0951023483836, 0.937129344143, -0.335773935375)-27.4267100284, -41.5426436822, 55.6589900053
3given(-0.987100613449, -0.150638668597, -0.0542251828212), (-0.101681139137, 0.328245330232, 0.939103801038), (-0.123666183221, 0.932503616457, -0.339328278254)-28.0951018488, -42.6460114512, 54.7086068801

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21287.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903
#2: Protein Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)


Mass: 22487.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364


Mass: 1711.996 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTD1

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Non-polymers , 3 types, 202 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M SPG pH 4.6, 25 % PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→55.11 Å / Num. obs: 60213 / % possible obs: 99.9 % / Redundancy: 27.9 % / Biso Wilson estimate: 44.49 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.0663 / Rrim(I) all: 0.351 / Net I/σ(I): 9.39
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 4.163 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 5910 / CC1/2: 0.517 / CC star: 0.914 / Rpim(I) all: 0.818 / Rrim(I) all: 4.244 / % possible all: 98.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→55.11 Å / SU ML: 0.2457 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.2058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 2972 4.95 %
Rwork0.2072 57057 -
obs0.2088 60029 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→55.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 32 196 6564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556568
X-RAY DIFFRACTIONf_angle_d0.81638928
X-RAY DIFFRACTIONf_chiral_restr0.0538954
X-RAY DIFFRACTIONf_plane_restr0.00681171
X-RAY DIFFRACTIONf_dihedral_angle_d14.40652420
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.645797162631
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.834152045292
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.841456506443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.3761290.37392642X-RAY DIFFRACTION98.05
2.24-2.270.38161370.36242672X-RAY DIFFRACTION99.65
2.27-2.320.39961410.34392715X-RAY DIFFRACTION99.86
2.32-2.360.34021510.32892632X-RAY DIFFRACTION99.36
2.36-2.410.36721390.32712699X-RAY DIFFRACTION99.27
2.41-2.460.36741580.31182623X-RAY DIFFRACTION99.43
2.46-2.520.31021350.29292716X-RAY DIFFRACTION99.51
2.52-2.580.33151340.28032664X-RAY DIFFRACTION99.89
2.58-2.650.31381520.27642692X-RAY DIFFRACTION99.75
2.65-2.730.2871290.25542718X-RAY DIFFRACTION99.65
2.73-2.820.31811330.23742693X-RAY DIFFRACTION99.61
2.82-2.920.29731390.23172688X-RAY DIFFRACTION99.72
2.92-3.030.26341310.24822718X-RAY DIFFRACTION99.82
3.03-3.170.2681660.25292708X-RAY DIFFRACTION99.86
3.17-3.340.28371530.22982709X-RAY DIFFRACTION99.76
3.34-3.550.2241500.20212725X-RAY DIFFRACTION99.86
3.55-3.820.22241420.19262726X-RAY DIFFRACTION99.93
3.82-4.210.21931240.17112770X-RAY DIFFRACTION99.97
4.21-4.820.16111300.13542796X-RAY DIFFRACTION100
4.82-6.070.14561290.14752831X-RAY DIFFRACTION99.97
6.07-55.110.19891700.16772920X-RAY DIFFRACTION99.68
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)
13.41306561692-2.004946320090.5710983667485.789477476323.695992376279.08926684613-0.0693858623655-0.4323465361880.08367447366722.17331997147-0.00377299804374-0.9187753706610.346934005147-0.8925369947970.1824944775350.8691755987750.0611733015136-0.1504573961390.8206058845570.04640806999070.364803958747-24.2331339929-13.845952873839.7575965678
22.02534018188-0.6030063753451.008236006764.496811594371.297632949924.66533812211-0.01107991001740.0177068976092-0.100865866451-0.0372451074946-0.0371030123462-0.1736688207270.348850243088-0.04450543981750.08057110936680.510301207402-0.02831571091190.002681264787790.4294274815620.008125432342470.297896402062-21.5521281524-26.91957422696.99761027991
34.396050415551.110826084481.787156039022.18063861530.3693084997042.38864327633-0.5854905252020.158952400350.682304897904-0.4597758805390.0531915282571-0.0718543315877-1.558670596370.1230790565640.417801662911.267169807350.019022938196-0.2415911628460.438019216147-0.03084031400190.537935104409-10.98327264826.0458952364125.3188051551
47.07603586231-4.247793928980.03797305894746.831264029612.871501637065.22867463010.101635357140.171534047103-0.8687353563480.282701218144-0.5082532765281.209734935350.692404088302-0.435918001730.3759904231150.430980348396-0.153908103438-0.0201899605410.648299492373-0.05931280482840.3747926213-31.115738721-30.20541174534.70150630129
54.38556339731.48390274028-2.901867980035.56681828504-3.045303164815.22972104766-0.2785296884610.302952076659-0.17121560249-0.117110993160.1449184262940.08076561979120.281109381483-0.3820417129740.1387572246550.4523907951920.0208916667227-0.03271596224370.306955133581-0.02116006391990.2690811864761.55427048297-33.814992977331.561183958
64.18542588865-2.220653680330.5848514692187.652651750521.771683739339.008169162660.129687662103-0.5891376939740.2179889570980.2121584341740.153585981872-0.76184902896-0.1315045696781.1701556697-0.2817692047380.527761215838-0.0587195381634-0.0700829964480.4617987329920.0160433990650.413527471569.56347890153-32.176680735841.8631233483
70.942102986746-0.432954287588-0.4099488939973.213201977831.710528784182.50853790869-0.101034403675-0.03520229260.0814376069945-0.0954895383373-0.0358616454502-0.0404688064853-0.3779063941160.2229822053170.1213368367830.470153394364-0.008726378534180.02582513056220.2729246306440.01083856340.2900782569112.5161862736-20.506862842330.0236236269
81.0366491468-0.1786802321261.146862961196.597262729335.573849687745.89733998953-0.0289408492204-0.008427525622440.03761980484970.1196165401840.20080498805-0.153613130416-0.0852981402030.351417569029-0.04292874090730.4659424702930.0172567799530.02019633892810.2854687946010.01366743345930.3132293273660.0558529130018-15.686403990535.5189315914
91.141161777641.612618180331.416431602327.269542413894.094404333482.483687909230.08410570316460.2800733123930.274025943537-1.53241516805-0.6021510864050.374679855753-1.83420354751-0.6480375024160.6063563960350.8651604763940.117082878589-0.1311765342420.3037339441850.01376847483450.365620234018-3.76236185882-7.3702804983430.6981284638
102.032469473610.417093379265-1.230460730244.34337860248-1.575372433487.183290858370.170870815603-0.074218672892-0.0306208522381-0.335417273299-0.02965482441380.05455710234720.3884871573650.173398635175-0.1310034734220.4204840631740.0330511113435-0.05124453967780.253432070291-0.02365423184620.353184689998-2.87513874777-36.442555011727.8320126886
110.7976016574680.3420019491270.8725555476534.542369573840.789295277013.44073690650.1243973080670.135600911409-0.258592042534-0.307264402055-0.00298086104227-0.1025567335040.9942196753040.0373832602139-0.1166444494850.4227355890620.01218028076140.0171241948740.2862632993640.004282706112260.373086942607-2.99682744343-45.038387591130.7357262779
128.73790988946-5.22159147418-2.723843063165.830423449542.17047669065.86510235162-0.196153295727-0.4385202144120.09435967081620.5663836630480.003254153105850.420504452594-0.671870437203-0.9032485588690.2410024349480.6609654181390.0763740305827-0.02249422178580.4903402353-0.05276500853170.36000868074-18.122647079-14.903227072354.1405807188
135.684573547781.169742465422.023791287136.0862353884-1.363771461091.200421208640.164631796690.366451695183-0.309872737929-0.4936015462940.278586319048-0.4966537561911.120422690670.354803766215-0.426771795660.3709223861590.158305450670.01780113873840.327272358821-0.02695708919440.4946335446666.92704659293-44.975837655628.7892642793
145.535318697512.18774442704-0.3485881713336.8139224144-0.2871959866176.31342485351-0.00893535541064-0.193449295861-0.14454433191-0.0892293031282-0.2544958951950.2622845808770.725252356485-0.4315152276840.2788055568710.615972504702-0.0297904606478-0.03921354428870.524922180002-0.02389005100420.268443260287-27.1540934808-23.164043524814.3057117038
159.387788555092.951134242571.212091904385.637983375391.952402528385.440653803830.072001781777-1.122102422180.5823620759590.0640646110718-0.4372912930990.935531259683-0.391989921178-1.568212954110.3218958301360.6070972182230.217604577679-0.1207645158650.850415635198-0.1547253839830.483550320457-36.4254574083-14.448050327712.0737441517
166.69661337529-3.83992786153.810616641218.135358222220.08724040966646.208612286190.24419870582-0.471730315995-0.4037554163680.155428360628-0.1649941027760.3427312481921.03870597783-1.00811754076-0.1811206093380.722789352953-0.2635609603420.01904806150640.669795604522-0.03835130702540.433162421443-32.4673843978-36.151164219713.8291813286
173.168335991280.7328284856511.300451148533.860523665611.10696298944.58233582788-0.278488924635-0.7779774186660.45641098850.4631662360930.539622214059-0.3651326071480.19387084659-0.88706452874-0.07650768156710.8695330239640.0169770900825-0.03071243358420.696299091136-0.02064467220720.29766853294-23.6020165821-15.763889455830.5722963032
182.376347373690.3153761811010.2812191285084.564753348930.8299392892744.96220341372-0.0998591650773-0.5714648166070.313352307960.503560942353-0.05891048193360.492909449657-0.332764782441-1.551794505690.1417640249940.6708201493490.203678241702-0.05947486538050.882308498207-0.08976941042920.399785726545-30.5759609505-12.758945857733.1453183439
192.86412547151-1.75005148996-0.07101486946886.859923377053.143781292696.94132262377-0.248097253135-0.3861639536580.2804874531280.317257931626-0.04596267279520.490857146521-0.592670938995-0.8812322296390.3044672860890.6050822514930.184877911412-0.08689798986590.740263752262-0.07657728960360.384585317795-27.7472194626-12.66840515130.2409222353
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 167 through 182 )AA167 - 182166 - 181
22chain 'B' and (resid 2 through 97 )BB2 - 971 - 96
33chain 'B' and (resid 98 through 190 )BB98 - 19097 - 189
44chain 'C' and (resid 1 through 15 )CC1 - 151 - 15
55chain 'D' and (resid 2 through 26 )DD2 - 261 - 25
66chain 'D' and (resid 27 through 55 )DD27 - 5526 - 54
77chain 'D' and (resid 56 through 133 )DD56 - 13355 - 132
88chain 'D' and (resid 134 through 166 )DD134 - 166133 - 165
99chain 'D' and (resid 167 through 182 )DD167 - 182166 - 181
1010chain 'E' and (resid 0 through 32 )EE0 - 321 - 33
1111chain 'E' and (resid 33 through 97 )EE33 - 9734 - 98
1212chain 'E' and (resid 98 through 190 )EE98 - 19099 - 191
1313chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
1414chain 'A' and (resid 2 through 26 )AA2 - 261 - 25
1515chain 'A' and (resid 27 through 55 )AA27 - 5526 - 54
1616chain 'A' and (resid 56 through 76 )AA56 - 7655 - 75
1717chain 'A' and (resid 77 through 101 )AA77 - 10176 - 100
1818chain 'A' and (resid 102 through 133 )AA102 - 133101 - 132
1919chain 'A' and (resid 134 through 166 )AA134 - 166133 - 165

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