5zdz

Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+

Method: X-RAY DIFFRACTION

▼

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

mouse RAG1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 3	mouse RAG2 × 1 （P21784） HMGB1 A-B box × 1 （P63158） DNA (30-MER) × 1 DNA (39-MER) × 1 DNA chain M × 1 CALCIUM ION × 1 ZINC ION × 1 1,2-ETHANEDIOL × 2 POTASSIUM ION × 1 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 3	mouse RAG2 × 1 （P21784） ;DNA (5'-D(TPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ; × 1 DNA (54-MER) × 1 DNA chain L × 1 CALCIUM ION × 1 ZINC ION × 1 1,2-ETHANEDIOL × 1 POTASSIUM ION × 1 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 3–627； UniProt 384–1008 Author chain C； PDBConstruct 3–627； UniProt 384–1008

mouse RAG2

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 3 DNA 3	mouse RAG1 × 1 （P15919） HMGB1 A-B box × 1 （P63158） DNA (30-MER) × 1 DNA (39-MER) × 1 DNA chain M × 1 CALCIUM ION × 1 ZINC ION × 1 1,2-ETHANEDIOL × 2 POTASSIUM ION × 1 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 3	mouse RAG1 × 1 （P15919） ;DNA (5'-D(TPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ; × 1 DNA (54-MER) × 1 DNA chain L × 1 CALCIUM ION × 1 ZINC ION × 1 1,2-ETHANEDIOL × 1 POTASSIUM ION × 1 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 3–389； UniProt 1–387 Author chain D； PDBConstruct 3–389； UniProt 1–387

HMGB1 A-B box

Mus musculus

UniProt P63158

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 3	mouse RAG1 × 1 （P15919） mouse RAG2 × 1 （P21784） DNA (30-MER) × 1 DNA (39-MER) × 1 DNA chain M × 1 CALCIUM ION × 1 ZINC ION × 1 1,2-ETHANEDIOL × 2 POTASSIUM ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMGB1_MOUSE
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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5zdz
Deposition date deposition_date	2018-02-25
Structure title title	Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+
Keywords keywords	V(D)J recombination, RAG1-2-12RSS-23RSS complex, Hairpin forming complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5zdz__assembly_1__model_1

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

Download this curve (.dat)

5zdz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zdz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.56 Å
Rg (electron density)	45.69 Å
Total Rg	45.86 Å
Atom count	10695
Residues	1185
Excluded volume	183020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zdz__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5zdz__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Description description	mouse RAG1
Molecular weight formula_weight	71871.3 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	20360

GPVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

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	mouse RAG2
Molecular weight formula_weight	43225.7 kDa
Mutation mutation	M1V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPVSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQKIVSNSQTSTEDPGDSTPFEDSEEFCFS

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	HMGB1 A-B box
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	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(TPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3') ;
Molecular weight formula_weight	13979.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGCCAGAT

Entity 5 Entity 5 polymer

Description description	DNA (54-MER)
Molecular weight formula_weight	4864.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

AATCTGGCCTGTCTTA

Entity 6 Entity 6 polymer

Description description	DNA (30-MER)
Molecular weight formula_weight	4855.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TATCTGGCCTGTCTTA

Entity 7 Entity 7 polymer

Description description	DNA (39-MER)
Molecular weight formula_weight	16640.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGAT

Entity 8 Entity 8 polymer

Description description	DNA chain L
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 9 Entity 9 polymer

Description description	DNA chain M
Molecular weight formula_weight	12036.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M

CACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACC

Entity 10 Entity 10 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

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

Entity 12 Entity 12 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 13 Entity 13 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

▶

Unit-cell length a length_a	132.450 Å
Unit-cell length b length_b	109.000 Å
Unit-cell length c length_c	156.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	43.719 Å
R factor r_factor	0.2037
R_work r_work	0.2017
R_free r_free	0.2419

Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+

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

mouse RAG1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

mouse RAG2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HMGB1 A-B box

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

5zdz__assembly_1__model_1

5zdz__assembly_1__model_1 | I(q)

5zdz__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 (14)

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 polymer

Polymer Polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

7. Citations (1)