SAXSdb — 8p0v

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

Coiled-coil domain-containing protein 93

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Coiled-coil domain-containing protein 22 × 1 （O60826） DENN domain-containing protein 10 × 1 （Q8TCE6） Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） VPS35 endosomal protein-sorting factor-like × 1 （Q7Z3J2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCD93_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain K； PDBConstruct 1–631； UniProt 1–631

Coiled-coil domain-containing protein 22

OrganismNot specified

UniProt O60826

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Coiled-coil domain-containing protein 93 × 1 （Q567U6） DENN domain-containing protein 10 × 1 （Q8TCE6） Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） VPS35 endosomal protein-sorting factor-like × 1 （Q7Z3J2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCD22_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–627； UniProt 1–627

DENN domain-containing protein 10

OrganismNot specified

UniProt Q8TCE6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Coiled-coil domain-containing protein 93 × 1 （Q567U6） Coiled-coil domain-containing protein 22 × 1 （O60826） Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） VPS35 endosomal protein-sorting factor-like × 1 （Q7Z3J2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEN10_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–357； UniProt 1–357

Vacuolar protein sorting-associated protein 29

OrganismNot specified

UniProt Q9UBQ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Coiled-coil domain-containing protein 93 × 1 （Q567U6） Coiled-coil domain-containing protein 22 × 1 （O60826） DENN domain-containing protein 10 × 1 （Q8TCE6） VPS35 endosomal protein-sorting factor-like × 1 （Q7Z3J2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS29_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain N； PDBConstruct 1–182； UniProt 1–182

VPS35 endosomal protein-sorting factor-like

OrganismNot specified

UniProt Q7Z3J2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Coiled-coil domain-containing protein 93 × 1 （Q567U6） Coiled-coil domain-containing protein 22 × 1 （O60826） DENN domain-containing protein 10 × 1 （Q8TCE6） Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP35L_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain O； PDBConstruct 1–963； UniProt 1–963

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	8p0v
Deposition date deposition_date	2023-05-10
Structure title title	Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex
Keywords keywords	Coiled-coil, DENND domain, alpha solenoid, calponin homology, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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.

8p0v__assembly_1__model_1

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

Download this curve (.dat)

8p0v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8p0v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	57.12 Å
Rg (electron density)	58.27 Å
Total Rg	57.96 Å
Atom count	9072
Residues	1802
Excluded volume	147850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8p0v__assembly_1__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	Coiled-coil domain-containing protein 93
Molecular weight formula_weight	73319.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K
Atom count atom_count	9072

MGLPRGPEGQGLPEVETREDEEQNVKLTEILELLVAAGYFRARIKGLSPFDKVVGGMTWCITTCNFDVDVDLLFQENSTIGQKIALSEKIVSVLPRMKCPHQLEPHQIQGMDFIHIFPVVQWLVKRAIETKEEMGDYIRSYSVSQFQKTYSLPEDDDFIKRKEKAIKTVVDLSEVYKPRRKYKRHQGAEELLDEESRIHATLLEYGRRYGFSRQSKMEKAEDKKTALPAGLSATEKADAHEEDELRAAEEQRIQSLMTKMTAMANEESRLTASSVGQIVGLCSAEIKQIVSEYAEKQSELSAEESPEKLGTSQLHRRKVISLNKQIAQKTKHLEELRASHTSLQARYNEAKKTLTELKTYSEKLDKEQAALEKIESKADPSILQNLRALVAMNENLKSQEQEFKAHCREEMTRLQQEIENLKAERAPRGDEKTLSSGEPPGTLTSAMTHDEDLDRRYNMEKEKLYKIRLLQARRNREIAILHRKIDEVPSRAELIQYQKRFIELYRQISAVHKETKQFFTLYNTLDDKKVYLEKEISLLNSIHENFSQAMASPAARDQFLRQMEQIVEGIKQSRMKMEKKKQENKMRRDQLNDQYLELLEKQRLYFKTVKEFKEEGRKNEMLLSKVKAKAS

Entity 2 Entity 2 polymer

Description description	Coiled-coil domain-containing protein 22
Molecular weight formula_weight	70856.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MEEADRILIHSLRQAGTAVPPDVQTLRAFTTELVVEAVVRCLRVINPAVGSGLSPLLPLAMSARFRLAMSLAQACMDLGYPLELGYQNFLYPSEPDLRDLLLFLAERLPTDASEDADQPAGDSAILLRAIGSQIRDQLALPWVPPHLRTPKLQHLQGSALQKPFHASRLVVPELSSRGEPREFQASPLLLPVPTQVPQPVGRVASLLEHHALQLCQQTGRDRPGDEDWVHRTSRLPPQEDTRAQRQRLQKQLTEHLRQSWGLLGAPIQARDLGELLQAWGAGAKTGAPKGSRFTHSEKFTFHLEPQAQATQVSDVPATSRRPEQVTWAAQEQELESLREQLEGVNRSIEEVEADMKTLGVSFVQAESECRHSKLSTAEREQALRLKSRAVELLPDGTANLAKLQLVVENSAQRVIHLAGQWEKHRVPLLAEYRHLRKLQDCRELESSRRLAEIQELHQSVRAAAEEARRKEEVYKQLMSELETLPRDVSRLAYTQRILEIVGNIRKQKEEITKILSDTKELQKEINSLSGKLDRTFAVTDELVFKDAKKDDAVRKAYKYLAALHENCSQLIQTIEDTGTIMREVRDLEEQIETELGKKTLSNLEKIREDYRALRQENAGLLGRVREA

Entity 3 Entity 3 polymer

Description description	DENN domain-containing protein 10
Molecular weight formula_weight	40563.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAAAEVADTQLMLGVGLIEKDTNGEVLWVWCYPSTTATLRNLLLRKCCLTDENKLLHPFVFGQYRRTWFYITTIEVPDSSILKKVTHFSIVLTAKDFNPEKYAAFTRILCRMYLKHGSPVKMMESYIAVLTKGICQSEENGSFLSKDFDARKAYLAGSIKDIVSQFGMETVILHTALMLKKRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYVHLNADELEALQMCTGYVAGFVDLEVSNRPDLYDVFVNLAESEITIAPLAKEAMAMGKLHKEMGQLIVQSAEDPEKSESHVIQDIALKTREIFTNLAPFSEVSADGEKRVLNLEALKQKRFPPATENFLYHLAAAEQMLKI

Entity 4 Entity 4 polymer

Description description	Vacuolar protein sorting-associated protein 29
Molecular weight formula_weight	20531.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKP

Entity 5 Entity 5 polymer

Description description	VPS35 endosomal protein-sorting factor-like
Molecular weight formula_weight	109700.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MAVFPWHSRNRNYKAEFASCRLEAVPLEFGDYHPLKPITVTESKTKKVNRKGSTSSTSSSSSSSVVDPLSSVLDGTDPLSMFAATADPAALAAAMDSSRRKRDRDDNSVVGSDFEPWTNKRGEILARYTTTEKLSINLFMGSEKGKAGTATLAMSEKVRTRLEELDDFEEGSQKELLNLTQQDYVNRIEELNQSLKDAWASDQKVKALKIVIQCSKLLSDTSVIQFYPSKFVLITDILDTFGKLVYERIFSMCVDSRSVLPDHFSPENANDTAKETCLNWFFKIASIRELIPRFYVEASILKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGMEVAPHLKETLNKNFFDFLLTFKQIHGDTVQNQLVVQGVELPSYLPLYPPAMDWIFQCISYHAPEALLTEMMERCKKLGNNALLLNSVMSAFRAEFIATRSMDFIGMIKECDESGFPKHLLFRSLGLNLALADPPESDRLQILNEAWKVITKLKNPQDYINCAEVWVEYTCKHFTKREVNTVLADVIKHMTPDRAFEDSYPQLQLIIKKVIAHFHDFSVLFSVEKFLPFLDMFQKESVRVEVCKCIMDAFIKHQQEPTKDPVILNALLHVCKTMHDSVNALTLEDEKRMLSYLINGFIKMVSFGRDFEQQLSFYVESRSMFCNLEPVLVQLIHSVNRLAMETRKVMKGNHSRKTAAFVRACVAYCFITIPSLAGIFTRLNLYLHSGQVALANQCLSQADAFFKAAISLVPEVPKMINIDGKMRPSESFLLEFLCNFFSTLLIVPDHPEHGVLFLVRELLNVIQDYTWEDNSDEKIRIYTCVLHLLSAMSQETYLYHIDKVDSNDSLYGGDSKFLAENNKLCETVMAQILEHLKTLAKDEALKRQSSLGLSFFNSILAHGDLRNNKLNQLSVNLWHLAQRHGCADTRTMVKTLEYIKKQSKQPDMTHLTELALRLPLQTRT

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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	6.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	125000

Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex

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

Coiled-coil domain-containing protein 93

State in the Current Structure

Other States of the Same Protein in the Database

Coiled-coil domain-containing protein 22

State in the Current Structure

Other States of the Same Protein in the Database

DENN domain-containing protein 10

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 29

State in the Current Structure

Other States of the Same Protein in the Database

VPS35 endosomal protein-sorting factor-like

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

8p0v__assembly_1__model_1

8p0v__assembly_1__model_1 | I(q)

8p0v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

7. Citations (3)

Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex

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

Coiled-coil domain-containing protein 93

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Coiled-coil domain-containing protein 22

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DENN domain-containing protein 10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar protein sorting-associated protein 29

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VPS35 endosomal protein-sorting factor-like

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

8p0v__assembly_1__model_1

8p0v__assembly_1__model_1 | I(q)

8p0v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

7. Citations (3)