SAXSdb — 6z3m

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

Growth/differentiation factor 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	RGM domain family member B × 6 （Q6NW40） Neogenin × 2 （P97798） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	RGM domain family member B × 6 （Q6NW40） Neogenin × 2 （P97798） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 10	RGM domain family member B × 6 （Q6NW40） Neogenin × 2 （P97798） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GDF5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–117； UniProt 387–501 Author chain B； PDBConstruct 3–117； UniProt 387–501 Author chain G； PDBConstruct 3–117； UniProt 387–501 Author chain H； PDBConstruct 3–117； UniProt 387–501 Author chain M； PDBConstruct 3–117； UniProt 387–501 Author chain N； PDBConstruct 3–117； UniProt 387–501

RGM domain family member B

Homo sapiens

UniProt Q6NW40

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Growth/differentiation factor 5 × 2 （P43026） Neogenin × 2 （P97798） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	Growth/differentiation factor 5 × 2 （P43026） Neogenin × 2 （P97798） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 10	Growth/differentiation factor 5 × 2 （P43026） Neogenin × 2 （P97798） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RGMB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–363； UniProt 53–412 Author chain D； PDBConstruct 4–363； UniProt 53–412 Author chain I； PDBConstruct 4–363； UniProt 53–412 Author chain J； PDBConstruct 4–363； UniProt 53–412 Author chain O； PDBConstruct 4–363； UniProt 53–412 Author chain P； PDBConstruct 4–363； UniProt 53–412 Author chain S； PDBConstruct 4–363； UniProt 53–412 Author chain T； PDBConstruct 4–363； UniProt 53–412 Author chain U； PDBConstruct 4–363； UniProt 53–412 Author chain V； PDBConstruct 4–363； UniProt 53–412 Author chain W； PDBConstruct 4–363； UniProt 53–412 Author chain X； PDBConstruct 4–363； UniProt 53–412 Author chain c； PDBConstruct 4–363； UniProt 53–412 Author chain d； PDBConstruct 4–363； UniProt 53–412 Author chain i； PDBConstruct 4–363； UniProt 53–412 Author chain j； PDBConstruct 4–363； UniProt 53–412 Author chain o； PDBConstruct 4–363； UniProt 53–412 Author chain p； PDBConstruct 4–363； UniProt 53–412

Neogenin

Mus musculus

UniProt P97798

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Growth/differentiation factor 5 × 2 （P43026） RGM domain family member B × 6 （Q6NW40） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	Growth/differentiation factor 5 × 2 （P43026） RGM domain family member B × 6 （Q6NW40） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 10	Growth/differentiation factor 5 × 2 （P43026） RGM domain family member B × 6 （Q6NW40） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEO1_MOUSE
Isoform	P97798-4
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 4–244； UniProt 883–1123 Author chain F； PDBConstruct 4–244； UniProt 883–1123 Author chain K； PDBConstruct 4–244； UniProt 883–1123 Author chain L； PDBConstruct 4–244； UniProt 883–1123 Author chain Q； PDBConstruct 4–244； UniProt 883–1123 Author chain R； PDBConstruct 4–244； UniProt 883–1123

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	6z3m
Deposition date deposition_date	2020-05-21
Structure title title	Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).
Keywords keywords	;Repulsive Guidance Molecule, RGM, Bone Morphogenetic Protein, BMP, Growth Differentiation Factor 5, GDF5, Neogenin, axon guidance, TGFbeta signalling, brain development, iron metabolism, signaling protein ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

6z3m__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6z3m__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z3m__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	46.42 Å
Rg (electron density)	47.60 Å
Total Rg	47.45 Å
Atom count	8235
Residues	1071
Excluded volume	146080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z3m__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6z3m__assembly_2__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6z3m__assembly_3__model_1`	decameric （10）	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 (4)

Entity 1 Entity 1 polymer

Description description	Growth/differentiation factor 5
Molecular weight formula_weight	13405.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,H,M,N
Atom count atom_count	25210

MKRQGKRPSKNLKARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RGM domain family member B
Molecular weight formula_weight	41036.7 kDa
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,I,J,O,P,c,d,i,j,o,p,S,T,U,V,W,X

ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGDPHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHGCTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQVSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIFPSSGTKHHHHHH

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 polymer

Description description	Neogenin
Molecular weight formula_weight	28031.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,K,L,Q,R

ETGTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKALGSAGKGSRLPDLGSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH

Source Source

Source organism organism	Mus musculus
Common name common_name	House mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 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	9

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Unit-cell length a length_a	279.480 Å
Unit-cell length b length_b	279.480 Å
Unit-cell length c length_c	142.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	108

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	5.501 Å
Low-resolution limit resolution_low	69.870 Å
R factor r_factor	0.3310
R_work r_work	0.3257
R_free r_free	0.4282

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).

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

Growth/differentiation factor 5

State in the Current Structure

Other States of the Same Protein in the Database

RGM domain family member B

State in the Current Structure

Other States of the Same Protein in the Database

Neogenin

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

6z3m__assembly_2__model_1

6z3m__assembly_2__model_1 | I(q)

6z3m__assembly_2__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 (4)

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 non-polymer

7. Citations (1)

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).

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

Growth/differentiation factor 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RGM domain family member B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Neogenin

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

6z3m__assembly_2__model_1

6z3m__assembly_2__model_1 | I(q)

6z3m__assembly_2__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 (4)

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 non-polymer

7. Citations (1)