SAXSdb — 7l9p

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

Pachytene checkpoint protein 2 homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Mitotic spindle assembly checkpoint protein MAD2B × 4 （Q9UI95） Shieldin complex subunit 2, Shieldin complex subunit 3 chimera × 2 （Q6ZNX1,Q86V20） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCH2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–432； UniProt 2–432 Author chain B； PDBConstruct 2–432； UniProt 2–432 Author chain C； PDBConstruct 2–432； UniProt 2–432 Author chain D； PDBConstruct 2–432； UniProt 2–432 Author chain E； PDBConstruct 2–432； UniProt 2–432 Author chain F； PDBConstruct 2–432； UniProt 2–432

Mitotic spindle assembly checkpoint protein MAD2B

Homo sapiens

UniProt Q9UI95

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Pachytene checkpoint protein 2 homolog × 6 （Q15645） Shieldin complex subunit 2, Shieldin complex subunit 3 chimera × 2 （Q6ZNX1,Q86V20） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MD2L2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 2–211； UniProt 2–211 Author chain I； PDBConstruct 2–211； UniProt 2–211 Author chain J； PDBConstruct 2–211； UniProt 2–211 Author chain K； PDBConstruct 2–211； UniProt 2–211

Shieldin complex subunit 2, Shieldin complex subunit 3 chimera

Homo sapiens

UniProt Q6ZNX1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Pachytene checkpoint protein 2 homolog × 6 （Q15645） Mitotic spindle assembly checkpoint protein MAD2B × 4 （Q9UI95） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SHLD3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain X； PDBConstruct 33–89； UniProt 2–58 Author chain Y； PDBConstruct 33–89； UniProt 2–58

Shieldin complex subunit 2, Shieldin complex subunit 3 chimera

Homo sapiens

UniProt Q86V20

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Pachytene checkpoint protein 2 homolog × 6 （Q15645） Mitotic spindle assembly checkpoint protein MAD2B × 4 （Q9UI95） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SHLD2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain X； PDBConstruct 2–16； UniProt 5–19 Author chain Y； PDBConstruct 2–16； UniProt 5–19

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	7l9p
Deposition date deposition_date	2021-01-04
Structure title title	Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex
Keywords keywords	REV7, SHLD2, SHLD3, TRIP13, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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.

7l9p__assembly_1__model_1

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

Download this curve (.dat)

7l9p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7l9p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.04 Å
Rg (electron density)	52.24 Å
Total Rg	52.34 Å
Atom count	21908
Residues	2919
Excluded volume	391320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7l9p__assembly_1__model_1`	dodecameric （12）	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 (4)

Entity 1 Entity 1 polymer

Description description	Pachytene checkpoint protein 2 homolog
Molecular weight formula_weight	48562.5 kDa
Mutation mutation	E253Q
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	21908

SDEAVGDLKQALPCVAESPTVHVEVHQRGSSTAKKEDINLSVRKLLNRHNIVFGDYTWTEFDEPFLTRNVQSVSIIDTELKVKDSQPIDLSACTVALHIFQLNEDGPSSENLEEETENIIAANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDQVESLTAARNACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFVDRADIKQYIGPPSAAAIFKIYLSCLEELMKCQIIYPRQQLLTLRELEMIGFIENNVSKLSLLLNDISRKSEGLSGRVLRKLPFLAHALYVQAPTVTIEGFLQALSLAVDKQFEERKKLAAYI

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Mitotic spindle assembly checkpoint protein MAD2B
Molecular weight formula_weight	24323.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I,J,K

STTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGS

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Shieldin complex subunit 2, Shieldin complex subunit 3 chimera
Molecular weight formula_weight	10678.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,X

MSQVHIFWGAPIAPLKGSGSGSGSGSGSGSGSTTEVILHYRPCESDPTQLPKIAEKAIQDFPTRPLSRFIPWFPYDGSKLPLRPKRSPPASREEIMATL

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 BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	7l9pB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7l9pC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7l9pD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7l9pE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7l9pG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	7l9pI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	7l9pK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

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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	—

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

Resolution resolution	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	104023

Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex

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

Pachytene checkpoint protein 2 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Mitotic spindle assembly checkpoint protein MAD2B

State in the Current Structure

Other States of the Same Protein in the Database

Shieldin complex subunit 2, Shieldin complex subunit 3 chimera

State in the Current Structure

Other States of the Same Protein in the Database

Shieldin complex subunit 2, Shieldin complex subunit 3 chimera

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

7l9p__assembly_1__model_1

7l9p__assembly_1__model_1 | I(q)

7l9p__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 (4)

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 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)

Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex

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

Pachytene checkpoint protein 2 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mitotic spindle assembly checkpoint protein MAD2B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Shieldin complex subunit 2, Shieldin complex subunit 3 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

Shieldin complex subunit 2, Shieldin complex subunit 3 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7l9p__assembly_1__model_1

7l9p__assembly_1__model_1 | I(q)

7l9p__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 (4)

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 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)