SAXSdb — 6ymq

▼

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

Triggering receptor expressed on myeloid cells 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Single-chain variable 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Single-chain variable 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Single-chain variable 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Single-chain variable 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Single-chain variable 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Single-chain variable 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TREM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D000； PDBConstruct 4–116； UniProt 19–131 Author chain G； PDBConstruct 4–116； UniProt 19–131 Author chain H； PDBConstruct 4–116； UniProt 19–131 Author chain I； PDBConstruct 4–116； UniProt 19–131 Author chain J； PDBConstruct 4–116； UniProt 19–131 Author chain K； PDBConstruct 4–116； UniProt 19–131

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	6ymq
Deposition date deposition_date	2020-04-09
Structure title title	TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)
Keywords keywords	;scFv, complex, receptor, Alzheimer's, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6ymq__assembly_1__model_1

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

Download this curve (.dat)

6ymq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ymq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.47 Å
Rg (electron density)	21.85 Å
Total Rg	22.74 Å
Atom count	2646
Residues	343
Excluded volume	46503 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ymq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ymq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6ymq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6ymq__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6ymq__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6ymq__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Description description	Single-chain variable 4
Molecular weight formula_weight	26245.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15730

SMEVQLLESGGGLVQPGGSLRLSCAASGFTFSYYYMGWVRQAPGKGLEWVSGISPSSGYTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYYYGYYYSHMDYWGQGTLVTVSSGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSRSGLHTFGQGTKLEIK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Triggering receptor expressed on myeloid cells 2
Molecular weight formula_weight	14067.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,D000

ETGHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLADGTKHHHHHH

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 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

▶

Unit-cell length a length_a	167.510 Å
Unit-cell length b length_b	180.770 Å
Unit-cell length c length_c	125.510 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	3.070 Å
Low-resolution limit resolution_low	75.990 Å
R factor r_factor	0.2742
R_work r_work	0.2735
R_free r_free	0.2878

TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)

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

Triggering receptor expressed on myeloid cells 2

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

6ymq__assembly_1__model_1

6ymq__assembly_1__model_1 | I(q)

6ymq__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (2)

TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)

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

Triggering receptor expressed on myeloid cells 2

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

6ymq__assembly_1__model_1

6ymq__assembly_1__model_1 | I(q)

6ymq__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (2)