SAXSdb — 8pyr

▼

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

Cyclin-dependent kinase 7

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cyclin-H × 1 （P51946） CDK-activating kinase assembly factor MAT1 × 1 （P51948） Nanobody (VHH-RD7-04) × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-H × 1 （P51946） CDK-activating kinase assembly factor MAT1 × 1 （P51948） Nanobody (VHH-RD7-04) × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDK7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–346； UniProt 1–346 Author chain E； PDBConstruct 1–346； UniProt 1–346

Cyclin-H

Homo sapiens

UniProt P51946

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 7 × 1 （P50613） CDK-activating kinase assembly factor MAT1 × 1 （P51948） Nanobody (VHH-RD7-04) × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 7 × 1 （P50613） CDK-activating kinase assembly factor MAT1 × 1 （P51948） Nanobody (VHH-RD7-04) × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNH_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–323； UniProt 1–323 Author chain F； PDBConstruct 1–323； UniProt 1–323

CDK-activating kinase assembly factor MAT1

Homo sapiens

UniProt P51948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 7 × 1 （P50613） Cyclin-H × 1 （P51946） Nanobody (VHH-RD7-04) × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 7 × 1 （P50613） Cyclin-H × 1 （P51946） Nanobody (VHH-RD7-04) × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAT1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–82； UniProt 230–309 Author chain G； PDBConstruct 3–82； UniProt 230–309

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	8pyr
Deposition date deposition_date	2023-07-26
Structure title title	Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex
Keywords keywords	Cdk7, Cyclin H, Mat1, CDK activating kinase, kinase, phosphorylation, TRANSCRIPTION; TRANSCRIPTION
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.

8pyr__assembly_1__model_1

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

Download this curve (.dat)

8pyr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8pyr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.34 Å
Rg (electron density)	28.60 Å
Total Rg	29.36 Å
Atom count	5833
Residues	730
Excluded volume	104390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8pyr__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8pyr__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent kinase 7
Molecular weight formula_weight	39250.3 kDa
EC 编号 ec_number	2.7.11.22,2.7.11.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	12032

MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cyclin-H
Molecular weight formula_weight	37695.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKSKHEEEEWTDDDLVESL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	CDK-activating kinase assembly factor MAT1
Molecular weight formula_weight	9043.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

GSGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDAFSGLFWQPS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	Nanobody (VHH-RD7-04)
Molecular weight formula_weight	12443.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLVESGGGLVQPGGSLRLSCVASGFTFKNFYMGWVRQAPDKGLEWVATINSGGEIQSYADSVKGRFTISRDNAKNTLYLQMNNLRPEDTAVYYCSKQSSTPAKGQGTQVTVSS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	384

▶

Unit-cell length a length_a	119.860 Å
Unit-cell length b length_b	77.866 Å
Unit-cell length c length_c	121.872 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.31 °
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	2.150 Å
Low-resolution limit resolution_low	48.050 Å
R factor r_factor	0.2226
R_work r_work	0.2197
R_free r_free	0.2415

Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex

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

Cyclin-dependent kinase 7

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-H

State in the Current Structure

Other States of the Same Protein in the Database

CDK-activating kinase assembly factor MAT1

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

8pyr__assembly_1__model_1

8pyr__assembly_1__model_1 | I(q)

8pyr__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 (6)

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

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (2)

Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex

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

Cyclin-dependent kinase 7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cyclin-H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CDK-activating kinase assembly factor MAT1

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

8pyr__assembly_1__model_1

8pyr__assembly_1__model_1 | I(q)

8pyr__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 (6)

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

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (2)