6cik

Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+

Method: X-RAY DIFFRACTION

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

V(D)J recombination-activating protein 1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 5	V(D)J recombination-activating protein 2 × 2 （P21784） High mobility group protein B1 × 1 （P09429） Intact 12RSS substrate reverse strand × 1 Intact 12RSS substrate forward strand × 1 Nicked 23RSS intermediate reverse strand × 1 ;DNA (5'-D(APTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ; × 1 Nicked 23RSS intermediate forward strand × 1 ZINC ION × 2 MANGANESE (II) ION × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAG1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–625； UniProt 384–1008 Author chain C； PDBConstruct 1–625； UniProt 384–1008

V(D)J recombination-activating protein 2

Mus musculus

UniProt P21784

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 5	V(D)J recombination-activating protein 1 × 2 （P15919） High mobility group protein B1 × 1 （P09429） Intact 12RSS substrate reverse strand × 1 Intact 12RSS substrate forward strand × 1 Nicked 23RSS intermediate reverse strand × 1 ;DNA (5'-D(APTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ; × 1 Nicked 23RSS intermediate forward strand × 1 ZINC ION × 2 MANGANESE (II) ION × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAG2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–359； UniProt 1–359 Author chain D； PDBConstruct 1–359； UniProt 1–359

High mobility group protein B1

Homo sapiens

UniProt P09429

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 5	V(D)J recombination-activating protein 1 × 2 （P15919） V(D)J recombination-activating protein 2 × 2 （P21784） Intact 12RSS substrate reverse strand × 1 Intact 12RSS substrate forward strand × 1 Nicked 23RSS intermediate reverse strand × 1 ;DNA (5'-D(APTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ; × 1 Nicked 23RSS intermediate forward strand × 1 ZINC ION × 2 MANGANESE (II) ION × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMGB1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–163； UniProt 1–163

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	6cik
Deposition date deposition_date	2018-02-24
Structure title title	Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+
Keywords keywords	VDJ recombination, RSS, RAG1/2, RECOMBINATION, RECOMBINATION-DNA complex; RECOMBINATION/DNA
Experimental Method method	X-RAY DIFFRACTION

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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.

6cik__assembly_1__model_1

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

Download this curve (.dat)

6cik__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cik__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.21 Å
Rg (electron density)	45.57 Å
Total Rg	45.72 Å
Atom count	18697
Residues	2147
Excluded volume	320350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cik__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 (11)

Entity 1 Entity 1 polymer

Description description	V(D)J recombination-activating protein 1
Molecular weight formula_weight	71716.1 kDa
EC 编号 ec_number	3.1.-.-,2.3.2.27
Mutation mutation	E962Q
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	18735

VHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	V(D)J recombination-activating protein 2
Molecular weight formula_weight	40036.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQ

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	High mobility group protein B1
Molecular weight formula_weight	18897.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Intact 12RSS substrate reverse strand
Molecular weight formula_weight	12140.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGC

Entity 5 Entity 5 polymer

Description description	Intact 12RSS substrate forward strand
Molecular weight formula_weight	12194.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GCCTGTCTTACACAGTGATACAGCCCTTAACAAAAACCCG

Entity 6 Entity 6 polymer

Description description	Nicked 23RSS intermediate reverse strand
Molecular weight formula_weight	16978.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

AGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGA

Entity 7 Entity 7 polymer

Description description	;DNA (5'-D(APTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ;
Molecular weight formula_weight	4551.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCTGGCCTGTCTTA

Entity 8 Entity 8 polymer

Description description	Nicked 23RSS intermediate forward strand
Molecular weight formula_weight	12326.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M

CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCC

Entity 9 Entity 9 non-polymer

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

Entity 10 Entity 10 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

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Unit-cell length a length_a	156.423 Å
Unit-cell length b length_b	123.149 Å
Unit-cell length c length_c	186.327 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	37.842 Å
R factor r_factor	0.2109
R_work r_work	0.2089
R_free r_free	0.2489

Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+

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

High mobility group protein B1

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

6cik__assembly_1__model_1

6cik__assembly_1__model_1 | I(q)

6cik__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

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

Source Source

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 polymer

Polymer Polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)