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6axf

Structure of RasGRP2 in complex with Rap1B

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

RAS guanyl-releasing protein 2

Homo sapiens

UniProt Q7LDG7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
7 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count
8 Protein heterocomplex Heteromer Protein 2 Ras-related protein Rap-1b × 1 （P61224） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2ma2

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6axf 6axf 6axf 6axf 6axf 6axf 6axf 6axf

8 assemblies

View Construct and Data Evidence
UniProt name GRP2_HUMAN
Isoform Q7LDG7-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–397； UniProt 63–456 Author chain C； PDBConstruct 4–397； UniProt 63–456 Author chain E； PDBConstruct 4–397； UniProt 63–456 Author chain G； PDBConstruct 4–397； UniProt 63–456 Author chain I； PDBConstruct 4–397； UniProt 63–456 Author chain K； PDBConstruct 4–397； UniProt 63–456 Author chain M； PDBConstruct 4–397； UniProt 63–456 Author chain O； PDBConstruct 4–397； UniProt 63–456

Ras-related protein Rap-1b

Homo sapiens

UniProt P61224

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
7 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count
8 Protein heterocomplex Heteromer Protein 2 RAS guanyl-releasing protein 2 × 1 （Q7LDG7） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3brw

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3cf6 3cf6 4dxa 4hdo 4hdq 4m8n 4m8n 4mgi 4mgi 4mgk 4mgk 4mgy

38 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RAP1B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–169； UniProt 1–167 Author chain D； PDBConstruct 3–169； UniProt 1–167 Author chain F； PDBConstruct 3–169； UniProt 1–167 Author chain H； PDBConstruct 3–169； UniProt 1–167 Author chain J； PDBConstruct 3–169； UniProt 1–167 Author chain L； PDBConstruct 3–169； UniProt 1–167 Author chain N； PDBConstruct 3–169； UniProt 1–167 Author chain P； PDBConstruct 3–169； UniProt 1–167

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_id6axf
Deposition date deposition_date2017-09-06
Structure title titleStructure of RasGRP2 in complex with Rap1B
Keywords keywordsSIGNALING PROTEIN, PROTEIN BINDING; PROTEIN BINDING
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.

6axf__assembly_1__model_1

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

Download this curve (.dat)

6axf__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.

6axf__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）27.52 Å
Rg (electron density)26.42 Å
Total Rg27.11 Å
Atom count4388
Residues538
Excluded volume78470 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6axf__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6axf__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6axf__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6axf__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 6axf__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 6axf__assembly_6__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 6axf__assembly_7__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 6axf__assembly_8__model_1 dimeric （2） 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) 31 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6axfb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axfd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axff_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axfh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axfj_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axfl_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axfn_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6axfp_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (23 domains)

Domain ID domain_id6axfA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfH00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfI01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfJ00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfK01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfK02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfL00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfM01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfM02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfN00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6axfO01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily10 — Son of sevenless (SoS) protein Chain: S domain 1
Domain ID domain_id6axfO02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily10 — Ras guanine-nucleotide exchange factors catalytic domain
Domain ID domain_id6axfP00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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7. Citations (1)