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- PDB-5zdz: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+ -

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Basic information

Entry
Database: PDB / ID: 5zdz
TitleHairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+
Components
  • DNA (30-MER)
  • DNA (39-MER)
  • DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
  • DNA (54-MER)
  • DNA chain L
  • DNA chain M
  • HMGB1 A-B box
  • mouse RAG1
  • mouse RAG2
KeywordsDNA BINDING PROTEIN / V(D)J recombination / RAG1-2-12RSS-23RSS complex / Hairpin forming complex
Function / homology
Function and homology information


Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / crossed form four-way junction DNA binding / Pyroptosis / Advanced glycosylation endproduct receptor signaling / plasmacytoid dendritic cell activation / regulation of tolerance induction / Regulation of TLR by endogenous ligand ...Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / crossed form four-way junction DNA binding / Pyroptosis / Advanced glycosylation endproduct receptor signaling / plasmacytoid dendritic cell activation / regulation of tolerance induction / Regulation of TLR by endogenous ligand / regulation of T cell mediated immune response to tumor cell / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of myeloid cell differentiation / myeloid dendritic cell activation / DNA geometric change / mature B cell differentiation involved in immune response / TRAF6 mediated NF-kB activation / bent DNA binding / glycolipid binding / positive regulation of toll-like receptor 9 signaling pathway / DNA recombinase complex / positive regulation of glycogen catabolic process / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / endodeoxyribonuclease complex / neutrophil clearance / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / pre-B cell allelic exclusion / positive regulation of DNA ligation / RAGE receptor binding / eye development / positive regulation of organ growth / regulation of behavioral fear response / induction of positive chemotaxis / bubble DNA binding / V(D)J recombination / myeloid progenitor cell differentiation / myeloid cell differentiation / negative regulation of T cell apoptotic process / regulation of nucleotide-excision repair / macrophage activation involved in immune response / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / negative regulation of thymocyte apoptotic process / cellular response to interleukin-7 / glycogen catabolic process / phosphatidylinositol-3,5-bisphosphate binding / supercoiled DNA binding / apoptotic cell clearance / endothelial cell proliferation / DNA binding, bending / positive regulation of mesenchymal cell proliferation / positive regulation of T cell differentiation / regulation of T cell differentiation / organ growth / T cell lineage commitment / positive regulation of wound healing / B cell lineage commitment / protein kinase activator activity / positive regulation of sprouting angiogenesis / phosphatidylserine binding / T cell homeostasis / positive regulation of interferon-alpha production / phosphatidylinositol-3,4,5-trisphosphate binding / endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation / protein autoubiquitination / positive regulation of autophagy / response to glucocorticoid / four-way junction DNA binding / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interferon-beta production / methylated histone binding / Neutrophil degranulation / positive regulation of mitotic cell cycle / B cell differentiation / phosphatidylinositol binding / thymus development / positive regulation of interleukin-1 beta production / cytokine activity / lung development / peptide binding / base-excision repair / RING-type E3 ubiquitin transferase / visual learning / autophagy / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / ubiquitin-protein transferase activity / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / double-stranded RNA binding / chromatin organization / single-stranded DNA binding / heparin binding / chromosome
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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / Kelch-type beta propeller / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / DNA / DNA (> 10) / V(D)J recombination-activating protein 1 / V(D)J recombination-activating protein 2 / High mobility group protein B1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, M.S. / Chuenchor, W. / Chen, X. / Gellert, M. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
NIH 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 25, 2018Deposition site: PDBJ / Processing site: PDBJ
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 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mouse RAG1
B: mouse RAG2
C: mouse RAG1
D: mouse RAG2
N: HMGB1 A-B box
F: DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
I: DNA (54-MER)
J: DNA (30-MER)
G: DNA (39-MER)
L: DNA chain L
M: DNA chain M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,08220
Polymers310,60711
Non-polymers4759
Water2,306128
1
A: mouse RAG1
B: mouse RAG2
N: HMGB1 A-B box
J: DNA (30-MER)
G: DNA (39-MER)
M: DNA chain M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,79611
Polymers167,5286
Non-polymers2695
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-68 kcal/mol
Surface area67490 Å2
MethodPISA
2
C: mouse RAG1
D: mouse RAG2
F: DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
I: DNA (54-MER)
L: DNA chain L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2869
Polymers143,0795
Non-polymers2074
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-53 kcal/mol
Surface area57380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.450, 109.000, 156.050
Angle α, β, γ (deg.)90.00, 114.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 5 molecules ACBDN

#1: Protein mouse RAG1 / RAG-1


Mass: 71871.305 Da / Num. of mol.: 2 / Fragment: UNP residues 384-1008
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P15919, Hydrolases; Acting on ester bonds, RING-type E3 ubiquitin transferase
#2: Protein mouse RAG2 / RAG-2


Mass: 43225.711 Da / Num. of mol.: 2 / Fragment: UNP residues 1-387 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P21784
#3: Protein HMGB1 A-B box / High mobility group protein 1 / HMG-1


Mass: 18897.885 Da / Num. of mol.: 1 / Fragment: UNP residues 1-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hmgb1, Hmg-1, Hmg1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63158

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DNA chain , 6 types, 6 molecules FIJGLM

#4: DNA chain DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')


Mass: 13978.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (54-MER)


Mass: 4864.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (30-MER)


Mass: 4855.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (39-MER)


Mass: 16640.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA chain L


Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA chain M


Mass: 12036.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 137 molecules

#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 3.49 Å3/Da / Density % sol: 64.79 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 198942 / % possible obs: 99.6 % / Redundancy: 4.1 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→43.719 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.76
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2419 9495 5 %
Rwork0.2017 --
obs0.2037 190011 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→43.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16111 4093 18 128 20350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321095
X-RAY DIFFRACTIONf_angle_d1.15529327
X-RAY DIFFRACTIONf_dihedral_angle_d21.37511954
X-RAY DIFFRACTIONf_chiral_restr0.0613212
X-RAY DIFFRACTIONf_plane_restr0.0083083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83190.34853300.35026085X-RAY DIFFRACTION98
2.8319-2.86520.36693190.34196168X-RAY DIFFRACTION99
2.8652-2.90010.38623170.33046012X-RAY DIFFRACTION98
2.9001-2.93680.383030.32466127X-RAY DIFFRACTION98
2.9368-2.97540.32163300.30166077X-RAY DIFFRACTION99
2.9754-3.01620.34043430.29096156X-RAY DIFFRACTION98
3.0162-3.05930.37023030.30796068X-RAY DIFFRACTION98
3.0593-3.10490.31913260.29836089X-RAY DIFFRACTION98
3.1049-3.15340.33973320.28236144X-RAY DIFFRACTION98
3.1534-3.20510.30073250.25826077X-RAY DIFFRACTION98
3.2051-3.26040.28223150.23045994X-RAY DIFFRACTION98
3.2604-3.31960.27643290.22586107X-RAY DIFFRACTION98
3.3196-3.38350.2933110.22265974X-RAY DIFFRACTION97
3.3835-3.45250.25813110.22796032X-RAY DIFFRACTION97
3.4525-3.52750.26833080.2215992X-RAY DIFFRACTION96
3.5275-3.60960.25473220.22035944X-RAY DIFFRACTION97
3.6096-3.69980.26023030.21956000X-RAY DIFFRACTION96
3.6998-3.79980.26533260.21875965X-RAY DIFFRACTION96
3.7998-3.91150.24343140.20745942X-RAY DIFFRACTION96
3.9115-4.03770.23993070.19725913X-RAY DIFFRACTION96
4.0377-4.18190.23253110.18055919X-RAY DIFFRACTION95
4.1819-4.34920.22362980.18295936X-RAY DIFFRACTION96
4.3492-4.54690.22633080.17415906X-RAY DIFFRACTION95
4.5469-4.78630.24663060.16895907X-RAY DIFFRACTION95
4.7863-5.08580.18573160.16375974X-RAY DIFFRACTION96
5.0858-5.47780.18513280.16055999X-RAY DIFFRACTION97
5.4778-6.02780.22253200.17146042X-RAY DIFFRACTION97
6.0278-6.89710.23673200.18046056X-RAY DIFFRACTION98
6.8971-8.67840.18373200.16376082X-RAY DIFFRACTION98
8.6784-43.72480.20022940.17835829X-RAY DIFFRACTION94

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