6cij

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

Method: ELECTRON MICROSCOPY

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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 6	DNA (46-MER) × 1 ;DNA (5'-D(GPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ; × 1 ;DNA (5'-D(PCPTPGPGPAPTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ; × 1 DNA (60-MER) × 1 High mobility group protein B1 × 1 （P09429） DNA (30-MER) × 1 V(D)J recombination-activating protein 2 × 2 （P21784） DNA (41-MER) × 1 ZINC ION × 2 CALCIUM ION × 2	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 1–776； UniProt 265–1040 Author chain C； PDBConstruct 1–776； UniProt 265–1040

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 6	V(D)J recombination-activating protein 1 × 2 （P15919） DNA (46-MER) × 1 ;DNA (5'-D(GPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ; × 1 ;DNA (5'-D(PCPTPGPGPAPTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ; × 1 DNA (60-MER) × 1 DNA (30-MER) × 1 V(D)J recombination-activating protein 2 × 2 （P21784） DNA (41-MER) × 1 ZINC ION × 2 CALCIUM ION × 2	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	6
Chains and sequence ranges	Author chain N； PDBConstruct 1–163； UniProt 1–163

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 6	V(D)J recombination-activating protein 1 × 2 （P15919） DNA (46-MER) × 1 ;DNA (5'-D(GPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ; × 1 ;DNA (5'-D(PCPTPGPGPAPTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ; × 1 DNA (60-MER) × 1 High mobility group protein B1 × 1 （P09429） DNA (30-MER) × 1 DNA (41-MER) × 1 ZINC ION × 2 CALCIUM ION × 2	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	8
Chains and sequence ranges	Author chain B； PDBConstruct 1–520； UniProt 1–520 Author chain D； PDBConstruct 1–520； UniProt 1–520

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	6cij
Deposition date deposition_date	2018-02-24
Structure title title	Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
Keywords keywords	V(D)J recombination, RAG1/2, RSS, Immunity, RECOMBINATION, 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.

6cij__assembly_1__model_1

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

Download this curve (.dat)

6cij__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cij__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.87 Å
Rg (electron density)	47.77 Å
Total Rg	47.99 Å
Atom count	20413
Residues	2257
Excluded volume	348690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cij__assembly_1__model_1`	undecameric （11）	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	88670.8 kDa
EC 编号 ec_number	3.1.-.-,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	A,C
Atom count atom_count	20413

NCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKESKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNALKSSGFTMNSKETLGDPLGIEDSLESQDSMEF

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	DNA (46-MER)
Molecular weight formula_weight	14268.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGATC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ;
Molecular weight formula_weight	4880.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GATCTGGCCTGTCTTA

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PCPTPGPGPAPTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3') ;
Molecular weight formula_weight	6091.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CCTGGATCTGGCCTGTCTTA

Entity 5 Entity 5 polymer

Description description	DNA (60-MER)
Molecular weight formula_weight	18809.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGATCCAGG

Entity 6 Entity 6 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 K-12

Entity 7 Entity 7 polymer

Description description	DNA (30-MER)
Molecular weight formula_weight	9138.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

CACAGTGATACAGCCCTTAACAAAAACCCG

Entity 8 Entity 8 polymer

Description description	V(D)J recombination-activating protein 2
Molecular weight formula_weight	58158.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQKIVSNSQTSTEDPGDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARALQAPKRNPPLQKPPMKSLHKKGSGKVLTPAKKS

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 9 Entity 9 polymer

Description description	DNA (41-MER)
Molecular weight formula_weight	12655.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M

CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCCG

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	49624

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

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

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

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

6cij__assembly_1__model_1

6cij__assembly_1__model_1 | I(q)

6cij__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

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

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

7. Citations (1)