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- PDB-5ze2: Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ f... -

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Basic information

Entry
Database: PDB / ID: 5ze2
TitleHairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C
Components
  • (DNA (30-MER)) x 2
  • (DNA (31-MER)) x 2
  • (DNA (40-MER)) x 2
  • HMGB1 A-B box
  • mouse RAG1
  • mouse RAG2
KeywordsDNA BINDING PROTEIN / V(D)J recombination / RAG1-2-12RSS-23RSS complex / Hairpin complex
Function / homology
Function and homology information


Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / crossed form four-way junction DNA binding / Advanced glycosylation endproduct receptor signaling / Pyroptosis / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / Regulation of TLR by endogenous ligand / regulation of T cell mediated immune response to tumor cell ...Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / crossed form four-way junction DNA binding / Advanced glycosylation endproduct receptor signaling / Pyroptosis / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / Regulation of TLR by endogenous ligand / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / TRAF6 mediated NF-kB activation / mature B cell differentiation involved in immune response / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / bent DNA binding / positive regulation of toll-like receptor 9 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / B cell homeostatic proliferation / neutrophil clearance / negative regulation of T cell differentiation in thymus / positive regulation of glycogen catabolic process / DN2 thymocyte differentiation / pre-B cell allelic exclusion / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / positive regulation of organ growth / eye development / bubble DNA binding / induction of positive chemotaxis / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / myeloid progenitor cell differentiation / inflammatory response to antigenic stimulus / phosphatidylinositol-3,4-bisphosphate binding / macrophage activation involved in immune response / negative regulation of thymocyte apoptotic process / histone H3K4me3 reader activity / positive regulation of monocyte chemotaxis / regulation of nucleotide-excision repair / positive regulation of monocyte chemotactic protein-1 production / positive regulation of innate immune response / cellular response to interleukin-7 / endothelial cell proliferation / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / glycogen catabolic process / apoptotic cell clearance / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / DNA binding, bending / regulation of T cell differentiation / organ growth / positive regulation of T cell differentiation / T cell lineage commitment / positive regulation of wound healing / phosphatidylserine binding / B cell lineage commitment / positive regulation of sprouting angiogenesis / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / phosphatidylinositol-3,4,5-trisphosphate binding / T cell homeostasis / negative regulation of type II interferon production / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of blood vessel endothelial cell migration / T cell differentiation / protein kinase activator activity / positive regulation of blood vessel endothelial cell migration / protein autoubiquitination / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / transcription repressor complex / positive regulation of interleukin-12 production / positive regulation of autophagy / phosphatidylinositol binding / activation of innate immune response / positive regulation of mitotic cell cycle / lung development / positive regulation of interferon-beta production / response to glucocorticoid / thymus development
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / Recombination-activating protein 1 zinc-finger domain / : / 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 / HMG box A DNA-binding domain signature. / Recombination-activating protein 1 zinc-finger domain / : / 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) nonamer-binding domain / 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) / 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: 3.3 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
I: DNA (31-MER)
J: DNA (31-MER)
G: DNA (40-MER)
L: DNA (30-MER)
M: DNA (40-MER)
F: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,80022
Polymers311,18511
Non-polymers61511
Water18010
1
A: mouse RAG1
B: mouse RAG2
N: HMGB1 A-B box
I: DNA (31-MER)
G: DNA (40-MER)
M: DNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,45312
Polymers168,1156
Non-polymers3396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15920 Å2
ΔGint-83 kcal/mol
Surface area66370 Å2
MethodPISA
2
C: mouse RAG1
D: mouse RAG2
J: DNA (31-MER)
L: DNA (30-MER)
F: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,34710
Polymers143,0705
Non-polymers2765
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13270 Å2
ΔGint-70 kcal/mol
Surface area55010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.770, 108.120, 155.740
Angle α, β, γ (deg.)90.00, 114.45, 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): HET293T / 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
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 IJGLMF

#4: DNA chain DNA (31-MER)


Mass: 9536.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (31-MER)


Mass: 9527.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (40-MER)


Mass: 12257.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (30-MER)


Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (40-MER)


Mass: 12325.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA (30-MER)


Mass: 9306.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 21 molecules

#10: Chemical ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#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: obtained synthetically / Formula: K
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.27 Å3/Da / Density % sol: 62.39 %
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: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 121100 / % possible obs: 99.8 % / Redundancy: 5.3 % / Net I/σ(I): 11.5
Reflection shellResolution: 3.3→3.42 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: 3.3→37.627 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2366 5902 5.02 %
Rwork0.1996 --
obs0.2014 117466 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→37.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16107 4131 20 10 20268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221151
X-RAY DIFFRACTIONf_angle_d1.12729380
X-RAY DIFFRACTIONf_dihedral_angle_d21.57911971
X-RAY DIFFRACTIONf_chiral_restr0.0583218
X-RAY DIFFRACTIONf_plane_restr0.0073084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.33750.34112010.373718X-RAY DIFFRACTION99
3.3375-3.37670.36972030.34133794X-RAY DIFFRACTION100
3.3767-3.41790.33831920.32453683X-RAY DIFFRACTION100
3.4179-3.46110.31381870.32083778X-RAY DIFFRACTION100
3.4611-3.50660.34182080.29363745X-RAY DIFFRACTION99
3.5066-3.55460.31221910.28393673X-RAY DIFFRACTION100
3.5546-3.60530.39241990.28423768X-RAY DIFFRACTION100
3.6053-3.65910.34231970.27393725X-RAY DIFFRACTION100
3.6591-3.71620.27122110.26323788X-RAY DIFFRACTION100
3.7162-3.77710.28171880.2513678X-RAY DIFFRACTION100
3.7771-3.84220.28471950.24353753X-RAY DIFFRACTION100
3.8422-3.9120.25991990.22793752X-RAY DIFFRACTION99
3.912-3.98710.23912070.21333766X-RAY DIFFRACTION100
3.9871-4.06840.27281910.20423695X-RAY DIFFRACTION99
4.0684-4.15680.23492040.19273757X-RAY DIFFRACTION99
4.1568-4.25340.26761890.19643679X-RAY DIFFRACTION99
4.2534-4.35960.25311870.18833755X-RAY DIFFRACTION99
4.3596-4.47730.23881970.17453732X-RAY DIFFRACTION99
4.4773-4.60880.20922040.17343726X-RAY DIFFRACTION99
4.6088-4.75730.17162000.17583737X-RAY DIFFRACTION99
4.7573-4.92690.2442040.17493691X-RAY DIFFRACTION99
4.9269-5.12370.22642020.16963717X-RAY DIFFRACTION99
5.1237-5.35630.20251870.16463738X-RAY DIFFRACTION99
5.3563-5.63780.22481910.1773713X-RAY DIFFRACTION99
5.6378-5.98970.23582000.18993719X-RAY DIFFRACTION99
5.9897-6.45010.23221930.19273661X-RAY DIFFRACTION99
6.4501-7.09530.22551950.18553738X-RAY DIFFRACTION99
7.0953-8.1130.20561980.16333679X-RAY DIFFRACTION99
8.113-10.18780.16051930.14893669X-RAY DIFFRACTION98
10.1878-37.62980.20471890.18393537X-RAY DIFFRACTION94

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