3jbw

Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

V(D)J recombination-activating protein 1

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 6	V(D)J recombination-activating protein 2 × 2 （Q1RLW7） 12-RSS signal end forward strand × 1 Nicked 12-RSS intermediate reverse strand × 1 Nicked 23-RSS intermediate reverse strand × 1 Nicked 23-RSS intermediate forward strand × 1 5'-D(PGPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3' × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAG1_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–764； UniProt 271–1031 Author chain C； PDBConstruct 4–764； UniProt 271–1031

V(D)J recombination-activating protein 2

Danio rerio

UniProt Q1RLW7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 6	V(D)J recombination-activating protein 1 × 2 （O13033） 12-RSS signal end forward strand × 1 Nicked 12-RSS intermediate reverse strand × 1 Nicked 23-RSS intermediate reverse strand × 1 Nicked 23-RSS intermediate forward strand × 1 5'-D(PGPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3' × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1RLW7_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–533； UniProt 1–530 Author chain D； PDBConstruct 4–533； UniProt 1–530

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3jbw
Deposition date deposition_date	2015-10-21
Structure title title	Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)
Keywords keywords	;RAG1, RAG2, V(D)J recombination, Paired complex, Antigen receptor gene recombination, T and B cell development, RECOMBINATION-DNA complex ;; RECOMBINATION/DNA
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3jbw__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3jbw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jbw__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	47.71 Å
Rg (electron density)	46.22 Å
Total Rg	46.63 Å
Atom count	19997
Residues	2168
Excluded volume	340040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jbw__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	V(D)J recombination-activating protein 1
Molecular weight formula_weight	87684.1 kDa
EC 编号 ec_number	3.1.-.-, 6.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	19997

GGSRCQRDHLSTKLIPTEVPADLIRAVTCQVCDHLLSDPVQSPCRHLFCRLCIIRYTHALGPNCPTCNQHLNPSHLIKPAKFFLATLSSLPLLCPSEECSDWVRLDSFREHCLNHYREKESQEEQTPSEQNLDGYLPVNKGGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVKSVCLTLFLLALRAGNEHKQADELEAMMQGRGFGLHPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRNAEKELLPGFHQFEWQPALKNVSTSWDVGIIDGLSGWTVSVDDVPADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMCTSGFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTIMSISIRLEGEDDGITIFQEQKPNSELSCRPLCLMFVDESDHETLTAILGPVVAERKAMMESRLIISVGGLLRSFRFFFRGTGYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNMVLHSITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFMETQPTLDALHCDIGNATEFYKIFQDEIGEVYQKPNPSREERRRWRSTLDKQLRKKMKLKPVMRMNGNYARRLMTREAVEAVCELVPSEERREALLKLMDLYLQMKPVWRSTCPSRDCPDQLCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLAHVPEIVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELEDILKHHWLYTSKYLQKFMEAHKNS

Source Source

Source organism organism	Danio rerio
Common name common_name	zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	V(D)J recombination-activating protein 2
Molecular weight formula_weight	59435.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GGSMSLQPLTAVNCGSLVQPGFSLLDLEGDVYLFGQKGWPKRSCPTGIFGVRIKKGELKLRAISFSNNSSYLPPLRCPAIAHFEAQDGKPECYLIHGGRTPNNELSSSLYMLSVDSRGCNRKVTLRCEEKELVGDVPSARYGHTLSVINSRGKTACVLFGGRSYMPPTERTTQNWNSVVDCPPQVYLIDLEFGCCTAHTLPELTDGQSFHVALARQDCVYFLGGHILSSDCRPSRLIRLHVELLLGSPVLTCTILHEGLTITSAIASPIGYHEYIIFGGYQSETQKRMECTYVGLDDVGVHMESREPPQWTSEISHSRTWFGGSLGKGTALVAIPSEGNPTPPEAYHFYQVSFQKEQDGEATAQGGSQESTDFEDSAPLEDSEELYFGREPHELEYSSDVEGDTYNEEDEEDESQTGYWIKCCLSCQVDPNIWEPYYSTELTRPAMIFCSRGEGGHWVHAQCMELPESLLLQLSQDNSKYFCLDHGGLPKQEMTPPKQMLPVKRVPMKMTHRKAPVSLKMTPAKKTFLRRLFD

Source Source

Source organism organism	Danio rerio
Common name common_name	zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	12-RSS signal end forward strand
Molecular weight formula_weight	10439.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CACAGTGCTACAGACTGGAACAAAAACCCTGCAG

Entity 4 Entity 4 polymer

Description description	Nicked 12-RSS intermediate reverse strand
Molecular weight formula_weight	15439.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CTGCAGGGTTTTTGTTCCAGTCTGTAGCACTGTGTAAGACAGGCCAGATC

Entity 5 Entity 5 polymer

Description description	Nicked 23-RSS intermediate reverse strand
Molecular weight formula_weight	18870.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CTGCAGGGTTTTTGTACAGCCAGACAGTGGAGTACTACCACTGTGTAAGACAGGCCAGATC

Entity 6 Entity 6 polymer

Description description	Nicked 23-RSS intermediate forward strand
Molecular weight formula_weight	13806.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

CACAGTGGTAGTACTCCACTGTCTGGCTGTACAAAAACCCTGCAG

Entity 7 Entity 7 polymer

Description description	5'-D(PGPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3'
Molecular weight formula_weight	4880.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J

GATCTGGCCTGTCTTA

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.600 Å
Low-resolution limit resolution_low	4.600 Å
R factor r_factor	0.4735
R_work r_work	0.4735
R_free r_free	0.4642

Resolution resolution	4.60 Å
Resolution测定Method resolution_method	Projection matching
颗粒数 num_particles	14129

Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)

1. Protein Identity and Related Structures Protein Identity & Related Structures

V(D)J recombination-activating protein 1

State in the Current Structure

Other States of the Same Protein in the Database

V(D)J recombination-activating protein 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3jbw__assembly_1__model_1

3jbw__assembly_1__model_1 | I(q)

3jbw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)

Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)

1. Protein Identity and Related Structures Protein Identity & Related Structures

V(D)J recombination-activating protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V(D)J recombination-activating protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3jbw__assembly_1__model_1

3jbw__assembly_1__model_1 | I(q)

3jbw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)