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- PDB-6cil: PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLE... -

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Basic information

Entry
Database: PDB / ID: 6cil
TitlePRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+
Components
  • (Intact 12RSS substrate ...) x 2
  • (Intact 23RSS substrate ...) x 2
  • (V(D)J recombination-activating protein ...) x 2
  • High mobility group protein B1
KeywordsRECOMBINATION/DNA / VDJ recombination / RSS / RAG1/2 / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell differentiation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / neutrophil clearance / DN2 thymocyte differentiation / pre-B cell allelic exclusion / DNA geometric change / RAGE receptor binding / positive regulation of organ growth / positive regulation of interleukin-1 production / regulation of behavioral fear response / Regulation of TLR by endogenous ligand / bubble DNA binding / V(D)J recombination / negative regulation of T cell apoptotic process / alphav-beta3 integrin-HMGB1 complex / phosphatidylinositol-3,4-bisphosphate binding / Apoptosis induced DNA fragmentation / inflammatory response to antigenic stimulus / negative regulation of thymocyte apoptotic process / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / apoptotic cell clearance / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / DNA binding, bending / dendritic cell chemotaxis / IRAK4 deficiency (TLR2/4) / regulation of T cell differentiation / positive regulation of T cell differentiation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of DNA binding / organ growth / T cell lineage commitment / B cell lineage commitment / phosphatidylserine binding / chemoattractant activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / TRAF6 mediated NF-kB activation / DNA topological change / negative regulation of type II interferon production / negative regulation of blood vessel endothelial cell migration / Advanced glycosylation endproduct receptor signaling / positive regulation of interleukin-10 production / T cell differentiation / positive regulation of blood vessel endothelial cell migration / Pyroptosis / protein autoubiquitination / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / : / positive regulation of autophagy / phosphatidylinositol-4,5-bisphosphate binding / transcription repressor complex / positive regulation of interleukin-12 production / phosphatidylinositol binding / activation of innate immune response / B cell differentiation / thymus development / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / TAK1-dependent IKK and NF-kappa-B activation / visual learning / RING-type E3 ubiquitin transferase / double-strand break repair via nonhomologous end joining / autophagy / positive regulation of interleukin-6 production / neuron projection development / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / integrin binding / heterochromatin formation / double-strand break repair / single-stranded DNA binding / chromatin organization / T cell differentiation in thymus / ER-Phagosome pathway
Similarity search - Function
HMG box A DNA-binding domain, conserved site / Recombination-activating protein 1 zinc-finger domain / HMG box A DNA-binding domain signature. / : / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding ...HMG box A DNA-binding domain, conserved site / Recombination-activating protein 1 zinc-finger domain / HMG box A DNA-binding domain signature. / : / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Recombination activating protein 2 / RAG2 PHD domain / V-D-J recombination activating protein 2 / Recombination activating protein 2, PHD domain / Galactose oxidase/kelch, beta-propeller / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Kelch-type beta propeller / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / DNA / DNA (> 10) / High mobility group protein B1 / V(D)J recombination-activating protein 1 / V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.15 Å
AuthorsChuenchor, W. / Chen, X. / Kim, M.S. / Gellert, M. / Yang, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036147, DK036144, DK036167 United States
National Institutes of Health/Office of the Director United States
CitationJournal: Mol Cell / Year: 2018
Title: Cracking the DNA Code for V(D)J Recombination.
Authors: Min-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang /
Abstract: To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have ...To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.
History
DepositionFeb 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V(D)J recombination-activating protein 1
B: V(D)J recombination-activating protein 2
C: V(D)J recombination-activating protein 1
D: V(D)J recombination-activating protein 2
N: High mobility group protein B1
F: Intact 12RSS substrate reverse strand
I: Intact 12RSS substrate forward strand
G: Intact 23RSS substrate reverse strand
J: Intact 23RSS substrate forward strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,16113
Polymers300,9219
Non-polymers2414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The assembly was made by mixing of RAG1/2, 12RSS, 23RSS, and HMGB1 in 1:1.2:1.2:2 molar ratio. The tetrameric unit was then purified by gel filtration. The molecular weight ...Evidence: gel filtration, The assembly was made by mixing of RAG1/2, 12RSS, 23RSS, and HMGB1 in 1:1.2:1.2:2 molar ratio. The tetrameric unit was then purified by gel filtration. The molecular weight marker for gel filtration was used to determine the size of the complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.332, 118.830, 198.960
Angle α, β, γ (deg.)90.000, 100.590, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain D and (resid 1 through 4 or (resid 5...
21(chain B and (resid 1 through 38 or (resid 39...
12(chain C and (resid 408 through 503 or (resid 504...
22(chain A and ((resid 408 through 423 and (name N...
13(chain G and resid 33 through 50) or (chain J and resid 8 through 25)
23(chain F and resid 22 through 39) or (chain I and resid 8 through 25)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLNGLN(chain D and (resid 1 through 4 or (resid 5...DD1 - 41 - 4
121METMETMETMET(chain D and (resid 1 through 4 or (resid 5...DD55
131METMETARGARG(chain D and (resid 1 through 4 or (resid 5...DD1 - 3491 - 349
141METMETARGARG(chain D and (resid 1 through 4 or (resid 5...DD1 - 3491 - 349
151METMETARGARG(chain D and (resid 1 through 4 or (resid 5...DD1 - 3491 - 349
161METMETARGARG(chain D and (resid 1 through 4 or (resid 5...DD1 - 3491 - 349
211METMETLYSLYS(chain B and (resid 1 through 38 or (resid 39...BB1 - 381 - 38
221ARGARGARGARG(chain B and (resid 1 through 38 or (resid 39...BB3939
231METMETCYSCYS(chain B and (resid 1 through 38 or (resid 39...BB1 - 3501 - 350
241METMETCYSCYS(chain B and (resid 1 through 38 or (resid 39...BB1 - 3501 - 350
251METMETCYSCYS(chain B and (resid 1 through 38 or (resid 39...BB1 - 3501 - 350
261METMETCYSCYS(chain B and (resid 1 through 38 or (resid 39...BB1 - 3501 - 350
112LEULEULEULEU(chain C and (resid 408 through 503 or (resid 504...CC408 - 50325 - 120
122ARGARGARGARG(chain C and (resid 408 through 503 or (resid 504...CC504121
132LEULEUASNASN(chain C and (resid 408 through 503 or (resid 504...CC397 - 100714 - 624
142LEULEUASNASN(chain C and (resid 408 through 503 or (resid 504...CC397 - 100714 - 624
152LEULEUASNASN(chain C and (resid 408 through 503 or (resid 504...CC397 - 100714 - 624
162LEULEUASNASN(chain C and (resid 408 through 503 or (resid 504...CC397 - 100714 - 624
212LEULEUGLUGLU(chain A and ((resid 408 through 423 and (name N...AA408 - 42325 - 40
222LEULEUASNASN(chain A and ((resid 408 through 423 and (name N...AA408 - 100725 - 624
232LEULEUASNASN(chain A and ((resid 408 through 423 and (name N...AA408 - 100725 - 624
242LEULEUASNASN(chain A and ((resid 408 through 423 and (name N...AA408 - 100725 - 624
252LEULEUASNASN(chain A and ((resid 408 through 423 and (name N...AA408 - 100725 - 624
113DADADGDG(chain G and resid 33 through 50) or (chain J and resid 8 through 25)GH33 - 5033 - 50
123DCDCDTDT(chain G and resid 33 through 50) or (chain J and resid 8 through 25)JI8 - 256 - 23
213DADADGDG(chain F and resid 22 through 39) or (chain I and resid 8 through 25)FF22 - 3922 - 39
223DCDCDTDT(chain F and resid 22 through 39) or (chain I and resid 8 through 25)IG8 - 252 - 19

NCS ensembles :
ID
1
2
3

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Components

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V(D)J recombination-activating protein ... , 2 types, 4 molecules ACBD

#1: Protein V(D)J recombination-activating protein 1 / RAG-1


Mass: 71716.141 Da / Num. of mol.: 2 / Mutation: E962Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag1 / Plasmid: pLEXm / Details (production host): His(6)-MBP-PreScission / Production host: Homo sapiens (human)
References: UniProt: P15919, Hydrolases; Acting on ester bonds, RING-type E3 ubiquitin transferase
#2: Protein V(D)J recombination-activating protein 2 / RAG-2


Mass: 40036.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Plasmid: pLEXm / Details (production host): His(6)-MBP-PreScission / Production host: Homo sapiens (human) / References: UniProt: P21784

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Protein , 1 types, 1 molecules N

#3: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 18897.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P09429

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Intact 12RSS substrate ... , 2 types, 2 molecules FI

#4: DNA chain Intact 12RSS substrate reverse strand


Mass: 12429.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain Intact 12RSS substrate forward strand


Mass: 12194.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Intact 23RSS substrate ... , 2 types, 2 molecules GJ

#6: DNA chain Intact 23RSS substrate reverse strand


Mass: 16954.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: DNA chain Intact 23RSS substrate forward strand


Mass: 16937.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 4 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.15→50 Å / Num. obs: 27342 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 190.4 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.051 / Rrim(I) all: 0.104 / Χ2: 0.923 / Net I/σ(I): 13.6
Reflection shellResolution: 4.15→4.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1345 / CC1/2: 0.677 / Rpim(I) all: 0.511 / Rrim(I) all: 1.067 / Χ2: 0.742 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CIK

6cik


Resolution: 4.15→37.98 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1396 5.11 %Copy from intact/nicked structure
Rwork0.2061 ---
obs0.2073 27302 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 495.28 Å2 / Biso mean: 217.7642 Å2 / Biso min: 134.34 Å2
Refinement stepCycle: final / Resolution: 4.15→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14549 3690 4 0 18243
Biso mean--153.87 --
Num. residues----2076
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D2908X-RAY DIFFRACTION7.578TORSIONAL
12B2908X-RAY DIFFRACTION7.578TORSIONAL
21C5478X-RAY DIFFRACTION7.578TORSIONAL
22A5478X-RAY DIFFRACTION7.578TORSIONAL
31G708X-RAY DIFFRACTION7.578TORSIONAL
32F708X-RAY DIFFRACTION7.578TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.15-4.29810.27391300.24272532266298
4.2981-4.470.26631550.225225772732100
4.47-4.67310.25771600.202925652725100
4.6731-4.91890.26791390.20225942733100
4.9189-5.22640.2241340.182525712705100
5.2264-5.62880.24941510.200825812732100
5.6288-6.1930.24651330.19926152748100
6.193-7.08410.24181310.202825982729100
7.0841-8.90620.25261300.207426362766100
8.9062-37.98380.19781330.20762637277098

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