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- PDB-5ze0: Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS ... -

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Entry
Database: PDB / ID: 5ze0
TitleHairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+
Components
  • DNA (30-MER)
  • DNA (39-MER)
  • DNA (45-MER)
  • DNA (5'-D(*AP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
  • DNA (54-MER)
  • 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 / 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: 2.75 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 (45-MER)
I: DNA (5'-D(*AP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
J: DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
G: DNA (54-MER)
L: DNA (30-MER)
M: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,05020
Polymers310,60711
Non-polymers4449
Water3,045169
1
A: mouse RAG1
B: mouse RAG2
N: HMGB1 A-B box
J: DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
G: DNA (54-MER)
M: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,78011
Polymers167,5286
Non-polymers2535
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15140 Å2
ΔGint-67 kcal/mol
Surface area67500 Å2
MethodPISA
2
C: mouse RAG1
D: mouse RAG2
F: DNA (45-MER)
I: DNA (5'-D(*AP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
L: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2709
Polymers143,0795
Non-polymers1914
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-49 kcal/mol
Surface area57260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.440, 109.030, 156.850
Angle α, β, γ (deg.)90.00, 114.43, 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 383-1008
Source method: isolated from a genetically manipulated source
Details: after presicssion cleavage, GP sequence remains. / 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
Details: GP remains after prescission cleavage / 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 (45-MER)


Mass: 13978.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*AP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')


Mass: 4864.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')


Mass: 4855.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (54-MER)


Mass: 16640.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (30-MER)


Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA (39-MER)


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, 178 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: obtained synthetically / Formula: K
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM MES (pH 6.8), 15% PEG 3350, 200 mM 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: 2.75→50 Å / Num. obs: 208782 / % possible obs: 98.6 % / Redundancy: 4.2 % / Net I/σ(I): 11.25
Reflection shellResolution: 2.75→2.85 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→34.797 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.44
RfactorNum. reflection% reflection
Rfree0.234 10084 4.99 %
Rwork0.1994 --
obs0.2012 202142 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→34.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16106 4091 18 169 20384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221076
X-RAY DIFFRACTIONf_angle_d1.21229311
X-RAY DIFFRACTIONf_dihedral_angle_d21.14711946
X-RAY DIFFRACTIONf_chiral_restr0.1713209
X-RAY DIFFRACTIONf_plane_restr0.0073081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78120.3883330.36116425X-RAY DIFFRACTION97
2.7812-2.81390.34253380.34086390X-RAY DIFFRACTION97
2.8139-2.84820.38383540.32386313X-RAY DIFFRACTION97
2.8482-2.88430.33173350.30816437X-RAY DIFFRACTION98
2.8843-2.92220.34573440.3036409X-RAY DIFFRACTION97
2.9222-2.96220.32473330.2976465X-RAY DIFFRACTION98
2.9622-3.00450.32433470.28386422X-RAY DIFFRACTION98
3.0045-3.04930.35193360.28836459X-RAY DIFFRACTION98
3.0493-3.0970.31333470.27846408X-RAY DIFFRACTION98
3.097-3.14770.30393290.26126457X-RAY DIFFRACTION98
3.1477-3.20190.32853340.25486499X-RAY DIFFRACTION98
3.2019-3.26010.28673390.24096372X-RAY DIFFRACTION98
3.2601-3.32280.25913410.22986474X-RAY DIFFRACTION98
3.3228-3.39050.26533370.21776444X-RAY DIFFRACTION98
3.3905-3.46420.28023290.2196339X-RAY DIFFRACTION97
3.4642-3.54470.24333250.20926447X-RAY DIFFRACTION98
3.5447-3.63330.25813240.21436522X-RAY DIFFRACTION98
3.6333-3.73140.243280.20416387X-RAY DIFFRACTION97
3.7314-3.84110.2633390.21016371X-RAY DIFFRACTION98
3.8411-3.96490.23833310.1986334X-RAY DIFFRACTION96
3.9649-4.10640.20673310.17666405X-RAY DIFFRACTION98
4.1064-4.27050.17863360.16536497X-RAY DIFFRACTION98
4.2705-4.46450.16733290.15816338X-RAY DIFFRACTION97
4.4645-4.69930.17483410.15686418X-RAY DIFFRACTION98
4.6993-4.9930.18613440.15726365X-RAY DIFFRACTION97
4.993-5.37720.20883260.15736410X-RAY DIFFRACTION97
5.3772-5.91590.19813450.1626363X-RAY DIFFRACTION97
5.9159-6.76650.22193380.17566350X-RAY DIFFRACTION97
6.7665-8.50450.2113410.16466331X-RAY DIFFRACTION96
8.5045-34.80.18733300.16926207X-RAY DIFFRACTION94

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