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- PDB-5ze1: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM... -

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Basic information

Entry
Database: PDB / ID: 5ze1
TitleHairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C
Components
  • (DNA) x 6
  • 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 / crossed form four-way junction DNA binding / Pyroptosis / Advanced glycosylation endproduct receptor signaling / 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 / Pyroptosis / Advanced glycosylation endproduct receptor signaling / 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 / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / bent DNA binding / TAK1-dependent IKK and NF-kappa-B activation / neutrophil clearance / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / positive regulation of glycogen catabolic process / DN2 thymocyte differentiation / DNA geometric change / pre-B cell allelic exclusion / 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 / alphav-beta3 integrin-HMGB1 complex / negative regulation of T cell apoptotic process / myeloid cell differentiation / myeloid progenitor cell differentiation / phosphatidylinositol-3,4-bisphosphate binding / inflammatory response to antigenic stimulus / regulation of nucleotide-excision repair / macrophage activation involved in immune response / histone H3K4me3 reader activity / negative regulation of thymocyte apoptotic process / positive regulation of monocyte chemotaxis / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / cellular response to interleukin-7 / phosphatidylinositol-3,5-bisphosphate binding / endothelial cell proliferation / 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 / positive regulation of T cell differentiation / organ growth / 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 / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / negative regulation of type II interferon production / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / 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 / positive regulation of interleukin-12 production / positive regulation of autophagy / transcription repressor complex / phosphatidylinositol binding / activation of innate immune response / positive regulation of mitotic cell cycle / response to glucocorticoid / lung development / positive regulation of interferon-beta production / 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), 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) / 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 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
F: DNA
I: DNA
J: DNA
G: DNA
L: DNA
M: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,09720
Polymers310,60711
Non-polymers4919
Water93752
1
A: mouse RAG1
B: mouse RAG2
N: HMGB1 A-B box
J: DNA
G: DNA
M: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,80411
Polymers167,5286
Non-polymers2765
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-73 kcal/mol
Surface area67800 Å2
MethodPISA
2
C: mouse RAG1
D: mouse RAG2
F: DNA
I: DNA
L: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2939
Polymers143,0795
Non-polymers2144
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-56 kcal/mol
Surface area57540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.760, 108.600, 157.090
Angle α, β, γ (deg.)90.00, 114.20, 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): HET293T / 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


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


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


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


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


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


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, 61 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.: 1 / 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.: 52 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
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→50 Å / Num. obs: 163362 / % possible obs: 99.82 % / Redundancy: 5.2 % / Net I/σ(I): 13.4
Reflection shellResolution: 3→3.11 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→36.679 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.24
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.232 7888 4.96 %
Rwork0.1965 --
obs0.1982 159066 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→36.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16101 4093 12 52 20258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221087
X-RAY DIFFRACTIONf_angle_d1.17129310
X-RAY DIFFRACTIONf_dihedral_angle_d21.40711945
X-RAY DIFFRACTIONf_chiral_restr0.0593210
X-RAY DIFFRACTIONf_plane_restr0.0073082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.03410.3422710.35535079X-RAY DIFFRACTION100
3.0341-3.06980.3632580.34385052X-RAY DIFFRACTION100
3.0698-3.10720.35972600.32365128X-RAY DIFFRACTION100
3.1072-3.14660.36522720.32664981X-RAY DIFFRACTION100
3.1466-3.18790.3912620.33195093X-RAY DIFFRACTION100
3.1879-3.23160.36822430.30435069X-RAY DIFFRACTION100
3.2316-3.27770.26882600.28335019X-RAY DIFFRACTION100
3.2777-3.32660.31912800.26185073X-RAY DIFFRACTION100
3.3266-3.37860.29932580.24185069X-RAY DIFFRACTION100
3.3786-3.43390.22742700.23235020X-RAY DIFFRACTION100
3.4339-3.49310.28042950.23915121X-RAY DIFFRACTION99
3.4931-3.55650.31482510.24054979X-RAY DIFFRACTION100
3.5565-3.62490.28442700.23665090X-RAY DIFFRACTION100
3.6249-3.69880.28552540.2285014X-RAY DIFFRACTION99
3.6988-3.77920.23822570.2245061X-RAY DIFFRACTION100
3.7792-3.8670.25472620.20715073X-RAY DIFFRACTION100
3.867-3.96360.24592620.19625012X-RAY DIFFRACTION99
3.9636-4.07060.21872660.18655045X-RAY DIFFRACTION100
4.0706-4.19020.20832730.17545083X-RAY DIFFRACTION99
4.1902-4.32530.16962460.17075036X-RAY DIFFRACTION100
4.3253-4.47960.21222650.16615076X-RAY DIFFRACTION99
4.4796-4.65860.19412690.16864978X-RAY DIFFRACTION99
4.6586-4.87020.20212580.16625043X-RAY DIFFRACTION99
4.8702-5.12630.23112740.15725015X-RAY DIFFRACTION99
5.1263-5.44650.20192670.16335082X-RAY DIFFRACTION99
5.4465-5.86550.25932670.17624990X-RAY DIFFRACTION99
5.8655-6.45290.23852560.17955014X-RAY DIFFRACTION99
6.4529-7.380.2072650.17555025X-RAY DIFFRACTION99
7.38-9.27310.17542520.15215010X-RAY DIFFRACTION99
9.2731-36.68140.17242450.17014848X-RAY DIFFRACTION95

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