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6z3h

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 2)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Growth/differentiation factor 5

Homo sapiens

UniProt P43026

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 RGM domain family member B × 2 （Q6NW40） Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1waq 2bhk 7zjf

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3evs 3qb4 3qb4 3qb4 5hk5 5hk5 5hk5 5hk5 6z3g 6z3h 6z3j 6z3l

20 assemblies; showing the first 12

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

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 4 Growth/differentiation factor 5 × 2 （P43026） Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4bq6 4bq6 4bq7 4bq7 4bq8 4uhz 4ui0 4ui2 6z3h 6z3j 6z3m 6z3m

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RGMB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–87； UniProt 53–136

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_id6z3h
Deposition date deposition_date2020-05-20
Structure title titleRepulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 2)
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 methodX-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.

6z3h__assembly_1__model_1

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

Download this curve (.dat)

6z3h__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6z3h__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）23.41 Å
Rg (electron density)22.87 Å
Total Rg23.53 Å
Atom count2460
Residues322
Excluded volume43475 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6z3h__assembly_1__model_1 tetrameric （4） 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 (2)

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6z3ha_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.0 — automated matches
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7. Citations (1)