6dbi

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates

Method: ELECTRON MICROSCOPY

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

Recombination activating gene 1 - MBP chimera

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 DNA 6	Recombination activating gene 2 × 2 （Q1RLW7） Forward strand of 12-RSS signal end × 1 Reverse strand of 12-RSS × 1 Reverse strand of 23-RSS × 1 Forward strand of 23-RSS signal end × 1 Forward strand of coding flank × 2 ZINC ION × 2 CALCIUM ION × 4	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 399–1159； UniProt 271–1031 Author chain C； PDBConstruct 399–1159； UniProt 271–1031

Recombination activating gene 1 - MBP chimera

Danio rerio

UniProt P0AEX9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 DNA 6	Recombination activating gene 2 × 2 （Q1RLW7） Forward strand of 12-RSS signal end × 1 Reverse strand of 12-RSS × 1 Reverse strand of 23-RSS × 1 Forward strand of 23-RSS signal end × 1 Forward strand of coding flank × 2 ZINC ION × 2 CALCIUM ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–378； UniProt 29–392 Author chain C； PDBConstruct 15–378； UniProt 29–392

Recombination activating gene 2

Danio rerio

UniProt Q1RLW7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 DNA 6	Recombination activating gene 1 - MBP chimera × 2 （O13033,P0AEX9） Forward strand of 12-RSS signal end × 1 Reverse strand of 12-RSS × 1 Reverse strand of 23-RSS × 1 Forward strand of 23-RSS signal end × 1 Forward strand of coding flank × 2 ZINC ION × 2 CALCIUM ION × 4	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	6dbi
Deposition date deposition_date	2018-05-03
Structure title title	Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates
Keywords keywords	V(D)J recombination, synaptic RAG complex, nicked RSS intermediates, paired complex, 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.

6dbi__assembly_1__model_1

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

Download this curve (.dat)

6dbi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6dbi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.29 Å
Rg (electron density)	46.80 Å
Total Rg	47.18 Å
Atom count	20001
Residues	2168
Excluded volume	340240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6dbi__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 (9)

Entity 1 Entity 1 polymer

Description description	Recombination activating gene 1 - MBP chimera
Molecular weight formula_weight	131160.0 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A
Atom count atom_count	20001

MGSSHHHHHHGTKTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGTDYDIPTTLEVLFQGPLGSRCQRDHLSTKLIPTEVPADLIRAVTCQVCDHLLSDPVQSPCRHLFCRLCIIRYTHALGPNCPTCNQHLNPSHLIKPAKFFLATLSSLPLLCPSEECSDWVRLDSFREHCLNHYREKESQEEQTPSEQNLDGYLPVNKGGRPRQHLLSLTRRAQKHRLRDLKNQVKTFAEKEEGGDVKSVCLTLFLLALRAGNEHKQADELEAMMQGRGFGLHPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRNAEKELLPGFHQFEWQPALKNVSTSWDVGIIDGLSGWTVSVDDVPADTISRRFRYDVALVSALKDLEEDIMEGLRERALDDSMCTSGFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTIMSISIRLEGEDDGITIFQEQKPNSELSCRPLCLMFVDESDHETLTAILGPVVAERKAMMESRLIISVGGLLRSFRFFFRGTGYDEKMVREMEGLEASGSTYICTLCDSTRAEASQNMVLHSITRSHDENLERYEIWRKNPFSESADELRDRVKGVSAKPFMETQPTLDALHCDIGNATEFYKIFQDEIGEVYQKPNPSREERRRWRSTLDKQLRKKMKLKPVMRMNGNYARRLMTREAVEAVCELVPSEERREALLKLMDLYLQMKPVWRSTCPSRDCPDQLCQYSYNSQQFADLLSSMFKYRYDGKITNYLHKTLAHVPEIVERDGSIGAWASEGNESGNKLFRRFRKMNARQSKTFELEDILKHHWLYTSKYLQKFMEAHKNS

Source Source

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

Entity 2 Entity 2 polymer

Description description	Recombination activating gene 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	D,B

GGSMSLQPLTAVNCGSLVQPGFSLLDLEGDVYLFGQKGWPKRSCPTGIFGVRIKKGELKLRAISFSNNSSYLPPLRCPAIAHFEAQDGKPECYLIHGGRTPNNELSSSLYMLSVDSRGCNRKVTLRCEEKELVGDVPSARYGHTLSVINSRGKTACVLFGGRSYMPPTERTTQNWNSVVDCPPQVYLIDLEFGCCTAHTLPELTDGQSFHVALARQDCVYFLGGHILSSDCRPSRLIRLHVELLLGSPVLTCTILHEGLTITSAIASPIGYHEYIIFGGYQSETQKRMECTYVGLDDVGVHMESREPPQWTSEISHSRTWFGGSLGKGTALVAIPSEGNPTPPEAYHFYQVSFQKEQDGEATAQGGSQESTDFEDSAPLEDSEELYFGREPHELEYSSDVEGDTYNEEDEEDESQTGYWIKCCLSCQVDPNIWEPYYSTELTRPAMIFCSRGEGGHWVHAQCMELPESLLLQLSQDNSKYFCLDHGGLPKQEMTPPKQMLPVKRVPMKMTHRKAPVSLKMTPAKKTFLRRLFD

Source Source

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

Entity 3 Entity 3 polymer

Description description	Forward strand of 12-RSS signal end
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	Reverse strand of 12-RSS
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	Reverse strand of 23-RSS
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	Forward strand of 23-RSS signal end
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	Forward strand of coding flank
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

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

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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	3.400 Å
Low-resolution limit resolution_low	3.400 Å
R factor r_factor	0.4614
R_work r_work	0.4614
R_free r_free	0.4780

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	53109

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates

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

Recombination activating gene 1 - MBP chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Recombination activating gene 1 - MBP chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Recombination activating gene 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

6dbi__assembly_1__model_1

6dbi__assembly_1__model_1 | I(q)

6dbi__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 (9)

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

Entity 9 Entity 9 non-polymer

7. Citations (1)