SAXSdb — 21ks

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

Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 4	Protein Wnt-3a × 2 （P27467） Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR × 2 （A0A8V8TRG9,O75581） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FKB1A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 157–263； UniProt 2–108 Author chain D； PDBConstruct 157–263； UniProt 2–108 Author chain G； PDBConstruct 157–263； UniProt 2–108 Author chain H； PDBConstruct 157–263； UniProt 2–108 Author chain I； PDBConstruct 157–263； UniProt 2–108

Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A

Homo sapiens

UniProt Q9H461

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 4	Protein Wnt-3a × 2 （P27467） Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR × 2 （A0A8V8TRG9,O75581） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FZD8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 12–136； UniProt 31–155 Author chain D； PDBConstruct 12–136； UniProt 31–155 Author chain G； PDBConstruct 12–136； UniProt 31–155 Author chain H； PDBConstruct 12–136； UniProt 31–155 Author chain I； PDBConstruct 12–136； UniProt 31–155

Protein Wnt-3a

Mus musculus

UniProt P27467

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 4	Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A × 5 （P62942,Q9H461） Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR × 2 （A0A8V8TRG9,O75581） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WNT3A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–334； UniProt 19–352 Author chain E； PDBConstruct 1–334； UniProt 19–352

Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR

Homo sapiens

UniProt A0A8V8TRG9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 4	Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A × 5 （P62942,Q9H461） Protein Wnt-3a × 2 （P27467） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8V8TRG9_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 770–869； UniProt 1944–2043 Author chain F； PDBConstruct 770–869； UniProt 1944–2043

Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR

Homo sapiens

UniProt O75581

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 4	Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A × 5 （P62942,Q9H461） Protein Wnt-3a × 2 （P27467） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LRP6_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 9–749； UniProt 630–1370 Author chain F； PDBConstruct 9–749； UniProt 630–1370

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	21ks
Deposition date deposition_date	2025-12-17
Structure title title	A Wnt3a/Fzd8-CRD/LRP6-E3E4-LA complex with FKBP
Keywords keywords	Wnt3a-Fzd8-LRP6 extracellular complex, Cryo-EM structure, FKBP-stabilized Wnt3a homodimer, SIGNALING PROTEIN; SIGNALING 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.

21ks__assembly_1__model_1

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

Download this curve (.dat)

21ks__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

21ks__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.32 Å
Rg (electron density)	55.40 Å
Total Rg	55.45 Å
Atom count	19870
Residues	2480
Excluded volume	350490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`21ks__assembly_1__model_1`	nonameric （9）	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 (6)

Entity 1 Entity 1 polymer

Description description	Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A
Molecular weight formula_weight	29934.6 kDa
EC 编号 ec_number	5.2.1.8
Mutation mutation	C178S
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,D,H,I
Atom count atom_count	19870

HHHHHHHHASAKELACQEITVPLCKGIGYNYTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSPDLKFFLCSMYTPICLEDYKKPLPPCRSVCERAKAGCAPLMRQYGFAWPDRMRCDRLPEQGNPDTLCMDYNRTDGGGGSGGGGSGGGGSGGGGSGVQVETISPGDGRTFPKRGQTSVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLEDYKDDDDK

Source Source

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

Entity 2 Entity 2 polymer

Description description	Protein Wnt-3a
Molecular weight formula_weight	37438.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SYPIWWSLAVGPQYSSLSTQPILCASIPGLVPKQLRFCRNYVEIMPSVAEGVKAGIQECQHQFRGRRWNCTTVSNSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGSAAICGCSSRLQGSPGEGWKWGGCSEDIEFGGMVSREFADARENRPDARSAMNRHNNEAGRQAIASHMHLKCKCHGLSGSCEVKTCWWSQPDFRTIGDFLKDKYDSASEMVVEKHRESRGWVETLRPRYTYFKVPTERDLVYYEASPNFCEPNPETGSFGTRDRTCNVSSHGIDGCDLLCCGRGHNARTERRREKCHCVFHWCCYVSCQECTRVYDVHTCK

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR
Molecular weight formula_weight	98974.9 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	C840S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DYKDDDDKPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAVVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSCGEPPTCSPQQFTCFTGEIDCIPVAWRCDGFTECEDHSDELNCPVCSESQFQCASGQCIDGALRCNGDANCQDKSDEKNCEVLCLIDQFRCANGQCIGKHKKCDHNVDCSDKSDELDCYPTEEPAPQAGGGGSGGGGSGGGGSGGGGSELIRVAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWSRKYMKSGNVKDLTQAWDLYYHVFRRISKQHHHHHHHH

Source Source

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

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	RAPAMYCIN IMMUNOSUPPRESSANT DRUG
Molecular weight formula_weight	914.2 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.010 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.01 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	525970

A Wnt3a/Fzd8-CRD/LRP6-E3E4-LA complex with FKBP

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

Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein Wnt-3a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR

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

21ks__assembly_1__model_1

21ks__assembly_1__model_1 | I(q)

21ks__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)