SAXSdb — 9pvg

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

Malcavernin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Krev interaction trapped protein 1 × 1 （O00522）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Krev interaction trapped protein 1 × 1 （O00522）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCM2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–180； UniProt 51–228 Author chain B； PDBConstruct 3–180； UniProt 51–228 Author chain C； PDBConstruct 3–180； UniProt 51–228 Author chain D； PDBConstruct 3–180； UniProt 51–228

Krev interaction trapped protein 1

OrganismNot specified

UniProt O00522

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Malcavernin × 2 （Q9BSQ5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Malcavernin × 2 （Q9BSQ5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KRIT1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–29； UniProt 227–255 Author chain F； PDBConstruct 1–29； UniProt 227–255

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	9pvg
Deposition date deposition_date	2025-08-01
Last revision last_revision	2026-01-28
Structure title title	Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3
Keywords keywords	PTB domain, NPxY, NPxF, Cerebral Cavernous Malformations, CCM, protein-protein, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

9pvg__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pvg__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pvg__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.16 Å
Rg (electron density)	21.21 Å
Total Rg	22.01 Å
Atom count	2277
Residues	291
Excluded volume	40774 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pvg__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9pvg__assembly_2__model_1`	trimeric （3）	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 (2)

Entity 1 Entity 1 polymer

Description description	Malcavernin
Molecular weight formula_weight	19523.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4573

GSERVEPDRLLSDYIEKEVKYLGQLTSIPGYLNPSSRTEILHFIDNAKRAHQLPGHLTQEHDAVLSLSAYNVKLAWRDGEDIILRVPIHDIAAVSYVRDDAAHLVVLKTAQDPGISPSQSLCAESSRGLSAGSLSESAVGPVEACCLVILAAESKVAAEELCCLLGQVFQVVYTESTIDF

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 2 Entity 2 polymer

Description description	Krev interaction trapped protein 1
Molecular weight formula_weight	3352.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

TCIYNPLFGSDLQYTNRVDKVVINPYFGL

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Unit-cell length a length_a	45.198 Å
Unit-cell length b length_b	120.441 Å
Unit-cell length c length_c	67.778 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2497
R_work r_work	0.2470
R_free r_free	0.2967

Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3

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

Malcavernin

State in the Current Structure

Other States of the Same Protein in the Database

Krev interaction trapped protein 1

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

9pvg__assembly_2__model_1

9pvg__assembly_2__model_1 | I(q)

9pvg__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Citations (1)

Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3

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

Malcavernin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Krev interaction trapped 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pvg__assembly_2__model_1

9pvg__assembly_2__model_1 | I(q)

9pvg__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Citations (1)