SAXSdb — 9yrm

▼

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

Calmodulin-1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Intermembrane lipid transfer protein VPS13 × 1 （G0S3B8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149

Intermembrane lipid transfer protein VPS13

Thermochaetoides thermophila

UniProt G0S3B8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Calmodulin-1 × 1 （P0DP23）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS13_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 28–1417； UniProt 1–1390

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	9yrm
Deposition date deposition_date	2025-10-16
Structure title title	CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin
Keywords keywords	lipid transport protein; BLTP, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9yrm__assembly_1__model_1

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

Download this curve (.dat)

9yrm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yrm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.75 Å
Rg (electron density)	40.53 Å
Total Rg	40.77 Å
Atom count	9116
Residues	1128
Excluded volume	162570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yrm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Calmodulin-1
Molecular weight formula_weight	16852.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9116

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Entity 2 Entity 2 polymer

Description description	Intermembrane lipid transfer protein VPS13
Molecular weight formula_weight	162183.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDYKDHDGDYKDHDIDYKDDDDKLAAAMLEGLVAGLLNRFLGMYVKNFDPKQLKWEVWNGKVRLDNLELQREALDQLKLPINVIKGHLGHLVLHIPWKTLASEQVKINIEDVFLLASPKEEAEYDEDEEARRRHRLKMEKLDSAELLKERSQEGLSEEEQKRTQTFAQALVTKIVDNLQITIRNIHIRYEDAISAPGHPFALGITLEEFSAVSTDSDWTPAFITSIQSAHKLATLESLAIYWDTDAKLIGPGREPHEHSDQIPHDEMLKFFREMIAKGEADLSSEHQFILKPVSGQAKIEIDKTGSHTVPRYKANLLFDEIGVVLDDQQYRDALMMVDLFHYFIRHQEYKKFQPKGVTPKEDPRAWFRFAGNAVLSKIHERNRRWSWDYFRERRDDRRRYIELFKKTKQNIQLTPEEREDLDKLEWKLSYEDLRFWRSLARNQLKKENAEALKNKPPPQPQQQQGWLSWVWGSKPVQPQQEEQQGDENTRITEAQRKELYEVIQWDEKAALAAEIDVPRDSVRLLIETSLSTGSFTLRQNPHGDARDLISLHFDLFRAKGLTRPDSFLIDISLGGFRVNDNTTPDSLYKEIVRVKDAPNTEGQKRYSIADLELTVDEEAFFELQVEQHPLDGQGDVAVTMKLKPLEIIWNPNVVVGIADFFRPPERHMESINALLETANATVEGLRAQTRAGLQFALEEHKTVNAKLDLQAPLIILPESITTPNSTCLIVDAGHISVNSELVDKETMKQVQSTQDRPCTEEDLRRLEELMYDRFLVKLTSTQVLIGPSVEITKQQLVQRDEKRQLHIVDQINLDFVVAMSILPKAPNLTKLKISGHLPVLQVNASDSKYKHLMRIIEVAIPKLYDVEPVLAPSGSHPTIRPRLASDASTRSRRASFRKASTQFLQFVSQQQEIVLDESDSDDDSEKFEDAKDTSVDEQLRIQQRIFDFKFTVDQLRGSLYRSDPEGKHPDQLLVELVAENFGVEYHLRPYDMSAMVSLGSVTMDDFVENPPAEFKSIVSSGDIEDRKQARDLVRVKFVRVKKESPEFMSVYDGIETNVDVAISTINLVVTRKTLLTLLDFILVTFSNPQPAAPVATRMAVTDQESETNIIVQPPPIESGPIRVKVDLKSIRMILNNDGIRLATLSFNHADVGVYILGRYMRVSAKLGDLSLVDDVNLGVSEDSSLRQLVTIQGNELADFRYEYFDPDKPEKNPGYDSSIYLRAGSVKVNFIEEPFRKIVDFLVKFGKMQAIYNAARMAAANQAQQLQQSQSRIKFDIVVKTPIVVFPRVVMSPKPKRDVITAYLGEIYAQNAFVPLDDSEKADMAMKLTTGIRNIRLTSHFHYSEGRDEVLELIDHVDLGFTIIYAEHKEGIKRPDLEIEGSMSDFNLRITPYQLSALLAISQSVPTVFAADVEQHT

Source Source

Source organism organism	Thermochaetoides thermophila
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	Homo sapiens

▶

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	3.75 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	175364

CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin

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

Calmodulin-1

State in the Current Structure

Other States of the Same Protein in the Database

Intermembrane lipid transfer protein VPS13

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

9yrm__assembly_1__model_1

9yrm__assembly_1__model_1 | I(q)

9yrm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin

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

Calmodulin-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

Intermembrane lipid transfer protein VPS13

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

9yrm__assembly_1__model_1

9yrm__assembly_1__model_1 | I(q)

9yrm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)