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- PDB-4wwx: Crystal structure of the core RAG1/2 recombinase -

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Basic information

Entry
Database: PDB / ID: 4wwx
TitleCrystal structure of the core RAG1/2 recombinase
Components
  • V(D)J recombination-activating protein 1
  • V(D)J recombination-activating protein 2
KeywordsHydrolase / Ligase / V(D)J recombination / RAG1/2 / Recombination Activating Gene 1/2 / Crystal structure.
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / DNA recombinase complex / endodeoxyribonuclease complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / regulation of behavioral fear response / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination ...mature B cell differentiation involved in immune response / DNA recombinase complex / endodeoxyribonuclease complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / regulation of behavioral fear response / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / negative regulation of T cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of T cell differentiation / regulation of T cell differentiation / organ growth / T cell lineage commitment / B cell lineage commitment / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / protein autoubiquitination / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / B cell differentiation / thymus development / RING-type E3 ubiquitin transferase / visual learning / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell differentiation in thymus / chromatin organization / histone binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / adaptive immune response / Hydrolases; Acting on ester bonds / defense response to bacterium / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Helix Hairpins - #510 / 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 ...Helix Hairpins - #510 / 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 / Kelch-type beta propeller / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Helix Hairpins / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Helix non-globular / Zinc finger RING-type profile. / Zinc finger, RING-type / Special / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
V(D)J recombination-activating protein 1 / V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2001 Å
AuthorsKim, M.S. / Lapkouski, M. / Yang, W. / Gellert, M.
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the V(D)J recombinase RAG1-RAG2.
Authors: Kim, M.S. / Lapkouski, M. / Yang, W. / Gellert, M.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.type ..._citation.journal_id_CSD / _diffrn_detector.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: V(D)J recombination-activating protein 1
X: V(D)J recombination-activating protein 2
E: V(D)J recombination-activating protein 1
Y: V(D)J recombination-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,7226
Polymers219,5914
Non-polymers1312
Water0
1
B: V(D)J recombination-activating protein 1
X: V(D)J recombination-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8613
Polymers109,7962
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-11 kcal/mol
Surface area44090 Å2
MethodPISA
2
E: V(D)J recombination-activating protein 1
Y: V(D)J recombination-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8613
Polymers109,7962
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-4 kcal/mol
Surface area42640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.760, 180.050, 200.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and segid B
21chain E and segid E
12chain X and segid X
22chain Y and segid Y

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and segid BB0
211chain E and segid EE0
112chain X and segid XX0
212chain Y and segid YY0

NCS ensembles :
ID
1
2

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Components

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


Mass: 70923.203 Da / Num. of mol.: 2 / Fragment: UNP Residues 391-1008
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag1 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
References: UniProt: P15919, Hydrolases; Acting on ester bonds, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein V(D)J recombination-activating protein 2 / RAG-2


Mass: 38872.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: P21784
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES (pH 7.1), 10-15% PEG 3350, 200 mM tribasic ammonium citrate (pH 7.0), 100 mM KCl

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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: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 49907 / % possible obs: 98.82 % / Redundancy: 7.1 % / Net I/σ(I): 12.75

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3.2001→43.742 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1978 3.97 %
Rwork0.2055 47885 -
obs0.2077 49863 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.67 Å2 / Biso mean: 106.3628 Å2 / Biso min: 45.18 Å2
Refinement stepCycle: final / Resolution: 3.2001→43.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14976 0 2 0 14978
Biso mean--84.96 --
Num. residues----1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715304
X-RAY DIFFRACTIONf_angle_d1.11420654
X-RAY DIFFRACTIONf_chiral_restr0.0452248
X-RAY DIFFRACTIONf_plane_restr0.0052666
X-RAY DIFFRACTIONf_dihedral_angle_d14.4855751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B5776X-RAY DIFFRACTION9.876TORSIONAL
12E5776X-RAY DIFFRACTION9.876TORSIONAL
21X3018X-RAY DIFFRACTION9.876TORSIONAL
22Y3018X-RAY DIFFRACTION9.876TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.28010.42531450.351734153560100
3.2801-3.36870.34251350.304434223557100
3.3687-3.46780.33811470.277334053552100
3.4678-3.57970.31331350.266634263561100
3.5797-3.70760.31411470.262134173564100
3.7076-3.85590.29141530.242134613614100
3.8559-4.03130.29841260.226234103536100
4.0313-4.24370.31811390.2153435357499
4.2437-4.50930.26731450.20213415356099
4.5093-4.8570.22931500.1933404355499
4.857-5.3450.27571350.19313435357099
5.345-6.11670.24481450.20723415356098
6.1167-7.69950.25291450.19283418356397
7.6995-43.74650.17931310.15183407353894

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