6pts

NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state A)

Method: SOLUTION NMR

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

Apolipoprotein A-I

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	GTPase KRas × 1 （P01116） RAF proto-oncogene serine/threonine-protein kinase × 1 （P04049） 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 64 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 16 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APOA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–198； UniProt 68–265 Author chain C； PDBConstruct 1–198； UniProt 68–265

GTPase KRas

Homo sapiens

UniProt P01116

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Apolipoprotein A-I × 2 （P02647） RAF proto-oncogene serine/threonine-protein kinase × 1 （P04049） 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 64 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 16 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RASK_HUMAN
Isoform	P01116-2
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–185； UniProt 1–185

RAF proto-oncogene serine/threonine-protein kinase

Homo sapiens

UniProt P04049

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Apolipoprotein A-I × 2 （P02647） GTPase KRas × 1 （P01116） 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 64 O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 16 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAF1_HUMAN
Isoform	P04049-2
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–132； UniProt 56–187

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	6pts
Deposition date deposition_date	2019-07-16
Structure title title	NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state A)
Keywords keywords	protein-protein-bilayer complex, small GTPase, RAS-RAF-nanodisc complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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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.

6pts__assembly_1__model_8

Assembly 1 · Model 8 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6pts__assembly_1__model_8 | I(q)

100 plotted points; both axes use logarithmic scales.

6pts__assembly_1__model_8 | P(r) · Pending

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

Rg（Guinier）	43.71 Å
Rg (electron density)	39.31 Å
Total Rg	38.95 Å
Atom count	11566
Residues	713
Excluded volume	201590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6pts__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`6pts__assembly_1__model_2`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`6pts__assembly_1__model_3`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`6pts__assembly_1__model_4`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`6pts__assembly_1__model_5`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`6pts__assembly_1__model_6`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`6pts__assembly_1__model_7`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`6pts__assembly_1__model_8`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`6pts__assembly_1__model_9`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`6pts__assembly_1__model_10`	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 (8)

Entity 1 Entity 1 polymer

Description description	Apolipoprotein A-I
Molecular weight formula_weight	23080.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	115660

LKLLDNWDSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLN

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	GTPase KRas
Molecular weight formula_weight	21116.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKC

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	RAF proto-oncogene serine/threonine-protein kinase
Molecular weight formula_weight	15266.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

NTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLQEHKGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCVDW

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 BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	787.1 kDa
Source method src_method	syn
Copy count entity_count	64

Entity 5 Entity 5 non-polymer

Description description	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
Molecular weight formula_weight	788.0 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6ptsB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6ptsD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state A)

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

Apolipoprotein A-I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GTPase KRas

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RAF proto-oncogene serine/threonine-protein kinase

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

6pts__assembly_1__model_8

6pts__assembly_1__model_8 | I(q)

6pts__assembly_1__model_8 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (8)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)