SAXSdb — 8yym

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

Myeloid differentiation primary response protein MyD88

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 104	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MYD88_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–144； UniProt 153–296 Author chain AA； PDBConstruct 1–144； UniProt 153–296 Author chain AB； PDBConstruct 1–144； UniProt 153–296 Author chain AC； PDBConstruct 1–144； UniProt 153–296 Author chain B； PDBConstruct 1–144； UniProt 153–296 Author chain BA； PDBConstruct 1–144； UniProt 153–296 Author chain BB； PDBConstruct 1–144； UniProt 153–296 Author chain BC； PDBConstruct 1–144； UniProt 153–296 Author chain C； PDBConstruct 1–144； UniProt 153–296 Author chain CA； PDBConstruct 1–144； UniProt 153–296 Author chain CB； PDBConstruct 1–144； UniProt 153–296 Author chain CC； PDBConstruct 1–144； UniProt 153–296 Author chain D； PDBConstruct 1–144； UniProt 153–296 Author chain DA； PDBConstruct 1–144； UniProt 153–296 Author chain DB； PDBConstruct 1–144； UniProt 153–296 Author chain DC； PDBConstruct 1–144； UniProt 153–296 Author chain E； PDBConstruct 1–144； UniProt 153–296 Author chain EA； PDBConstruct 1–144； UniProt 153–296 Author chain EB； PDBConstruct 1–144； UniProt 153–296 Author chain EC； PDBConstruct 1–144； UniProt 153–296 Author chain F； PDBConstruct 1–144； UniProt 153–296 Author chain FA； PDBConstruct 1–144； UniProt 153–296 Author chain FB； PDBConstruct 1–144； UniProt 153–296 Author chain FC； PDBConstruct 1–144； UniProt 153–296 Author chain G； PDBConstruct 1–144； UniProt 153–296 Author chain GA； PDBConstruct 1–144； UniProt 153–296 Author chain GB； PDBConstruct 1–144； UniProt 153–296 Author chain GC； PDBConstruct 1–144； UniProt 153–296 Author chain H； PDBConstruct 1–144； UniProt 153–296 Author chain HA； PDBConstruct 1–144； UniProt 153–296 Author chain HB； PDBConstruct 1–144； UniProt 153–296 Author chain HC； PDBConstruct 1–144； UniProt 153–296 Author chain I； PDBConstruct 1–144； UniProt 153–296 Author chain IA； PDBConstruct 1–144； UniProt 153–296 Author chain IB； PDBConstruct 1–144； UniProt 153–296 Author chain IC； PDBConstruct 1–144； UniProt 153–296 Author chain J； PDBConstruct 1–144； UniProt 153–296 Author chain JA； PDBConstruct 1–144； UniProt 153–296 Author chain JB； PDBConstruct 1–144； UniProt 153–296 Author chain JC； PDBConstruct 1–144； UniProt 153–296 Author chain K； PDBConstruct 1–144； UniProt 153–296 Author chain KA； PDBConstruct 1–144； UniProt 153–296 Author chain KB； PDBConstruct 1–144； UniProt 153–296 Author chain KC； PDBConstruct 1–144； UniProt 153–296 Author chain L； PDBConstruct 1–144； UniProt 153–296 Author chain LA； PDBConstruct 1–144； UniProt 153–296 Author chain LB； PDBConstruct 1–144； UniProt 153–296 Author chain LC； PDBConstruct 1–144； UniProt 153–296 Author chain M； PDBConstruct 1–144； UniProt 153–296 Author chain MA； PDBConstruct 1–144； UniProt 153–296 Author chain MB； PDBConstruct 1–144； UniProt 153–296 Author chain MC； PDBConstruct 1–144； UniProt 153–296 Author chain N； PDBConstruct 1–144； UniProt 153–296 Author chain NA； PDBConstruct 1–144； UniProt 153–296 Author chain NB； PDBConstruct 1–144； UniProt 153–296 Author chain NC； PDBConstruct 1–144； UniProt 153–296 Author chain O； PDBConstruct 1–144； UniProt 153–296 Author chain OA； PDBConstruct 1–144； UniProt 153–296 Author chain OB； PDBConstruct 1–144； UniProt 153–296 Author chain OC； PDBConstruct 1–144； UniProt 153–296 Author chain P； PDBConstruct 1–144； UniProt 153–296 Author chain PA； PDBConstruct 1–144； UniProt 153–296 Author chain PB； PDBConstruct 1–144； UniProt 153–296 Author chain PC； PDBConstruct 1–144； UniProt 153–296 Author chain Q； PDBConstruct 1–144； UniProt 153–296 Author chain QA； PDBConstruct 1–144； UniProt 153–296 Author chain QB； PDBConstruct 1–144； UniProt 153–296 Author chain QC； PDBConstruct 1–144； UniProt 153–296 Author chain R； PDBConstruct 1–144； UniProt 153–296 Author chain RA； PDBConstruct 1–144； UniProt 153–296 Author chain RB； PDBConstruct 1–144； UniProt 153–296 Author chain RC； PDBConstruct 1–144； UniProt 153–296 Author chain S； PDBConstruct 1–144； UniProt 153–296 Author chain SA； PDBConstruct 1–144； UniProt 153–296 Author chain SB； PDBConstruct 1–144； UniProt 153–296 Author chain SC； PDBConstruct 1–144； UniProt 153–296 Author chain T； PDBConstruct 1–144； UniProt 153–296 Author chain TA； PDBConstruct 1–144； UniProt 153–296 Author chain TB； PDBConstruct 1–144； UniProt 153–296 Author chain TC； PDBConstruct 1–144； UniProt 153–296 Author chain U； PDBConstruct 1–144； UniProt 153–296 Author chain UA； PDBConstruct 1–144； UniProt 153–296 Author chain UB； PDBConstruct 1–144； UniProt 153–296 Author chain UC； PDBConstruct 1–144； UniProt 153–296 Author chain V； PDBConstruct 1–144； UniProt 153–296 Author chain VA； PDBConstruct 1–144； UniProt 153–296 Author chain VB； PDBConstruct 1–144； UniProt 153–296 Author chain VC； PDBConstruct 1–144； UniProt 153–296 Author chain W； PDBConstruct 1–144； UniProt 153–296 Author chain WA； PDBConstruct 1–144； UniProt 153–296 Author chain WB； PDBConstruct 1–144； UniProt 153–296 Author chain WC； PDBConstruct 1–144； UniProt 153–296 Author chain X； PDBConstruct 1–144； UniProt 153–296 Author chain XA； PDBConstruct 1–144； UniProt 153–296 Author chain XB； PDBConstruct 1–144； UniProt 153–296 Author chain XC； PDBConstruct 1–144； UniProt 153–296 Author chain Y； PDBConstruct 1–144； UniProt 153–296 Author chain YA； PDBConstruct 1–144； UniProt 153–296 Author chain YB； PDBConstruct 1–144； UniProt 153–296 Author chain YC； PDBConstruct 1–144； UniProt 153–296 Author chain Z； PDBConstruct 1–144； UniProt 153–296 Author chain ZA； PDBConstruct 1–144； UniProt 153–296 Author chain ZB； PDBConstruct 1–144； UniProt 153–296 Author chain ZC； PDBConstruct 1–144； UniProt 153–296

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	8yym
Deposition date deposition_date	2024-04-04
Structure title title	Cryo-EM structure of cylindrical fiber of MyD88 TIR
Keywords keywords	signaling protein, innate immunity, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

8yym__assembly_1__model_1

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

Download this curve (.dat)

8yym__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yym__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	140.00 Å
Total Rg	140.00 Å
Atom count	115856
Residues	14040
Excluded volume	2097100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yym__assembly_1__model_1`	104-meric （104）	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 (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	triclinic

Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	26680

Description description	Myeloid differentiation primary response protein MyD88
Molecular weight formula_weight	16841.8 kDa
Source method src_method	man
Copy count entity_count	104

Polymer type type	polypeptide(L)
Chain IDs strand_id	;A,AA,AB,AC,B,BA,BB,BC,C,CA,CB,CC,D,DA,DB,DC,E,EA,EB,EC,F,FA,FB,FC,G,GA,GB,GC,H,HA,HB,HC,I,IA,IB,IC,J,JA,JB,JC,K,KA,KB,KC,L,LA,LB,LC,M,MA,MB,MC,N,NA,NB,NC,O,OA,OB,OC,P,PA,PB,PC,Q,QA,QB,QC,R,RA,RB,RC,S,SA,SB,SC,T,TA,TB,TC,U,UA,UB,UC,V,VA,VB,VC,W,WA,WB,WC,X,XA,XB,XC,Y,YA,YB,YC,Z,ZA,ZB,ZC ;
Atom count atom_count	115856

Cryo-EM structure of cylindrical fiber of MyD88 TIR

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

Myeloid differentiation primary response protein MyD88

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

8yym__assembly_1__model_1

8yym__assembly_1__model_1 | I(q)

8yym__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (2)

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Cryo-EM structure of cylindrical fiber of MyD88 TIR

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

Myeloid differentiation primary response protein MyD88

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

8yym__assembly_1__model_1

8yym__assembly_1__model_1 | I(q)

8yym__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (2)