SAXSdb — 8gmj

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

ATP-dependent translocase ABCB1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–1280	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8GMJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6C0V Molecular structure of human P-glycoprotein in the ATP-bound, outward-facing conformation Deposited 2018-01-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Mutation：E556Q, E1201Q	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6QEX Nanodisc reconstituted human ABCB1 in complex with UIC2 fab and taxol Deposited 2019-01-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CLR CHOLESTEROL × 16 TA1 TAXOL × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
7A65 Nanodisc reconstituted, drug-free human ABCB1 in complex with MRK16 Fab Deposited 2020-08-25	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	CLR CHOLESTEROL × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7A69 Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and vincristine Deposited 2020-08-25	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	R1Q vincristine × 1 CLR CHOLESTEROL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7A6C Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and elacridar Deposited 2020-08-25	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	R0Z elacridar × 2 CLR CHOLESTEROL × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7A6E Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and tariquidar Deposited 2020-08-25	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	R1H tariquidar × 2 CLR CHOLESTEROL × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7A6F Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and zosuquidar Deposited 2020-08-25	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	ZQU Zosuquidar × 2 CLR CHOLESTEROL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7O9W Encequidar-bound human P-glycoprotein in complex with UIC2-Fab Deposited 2021-04-17	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	V5Q ~{N}-[2-[2-[4-[2-(6,7-dimethoxy-3,4-dihydro-1~{H}-isoquinolin-2-yl)ethyl]phenyl]-1,2,3,4-tetrazol-5-yl]-4,5-dimethoxy-phenyl]-4-oxidanylidene-2,3-dihydrochromene-2-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8GMG CryoEM structure of P-Glycoprotein in Apo state Deposited 2023-03-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8SA0 CryoEM structure of P-Glycoprotein in occluded closed state under continuous turnover conditions with verapamil Deposited 2023-03-30	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1274（1274 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 I6H Dexverapamil × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8SA1 CryoEM structure of P-Glycoprotein in inward facing 2 state under continuous turnover conditions with verapamil Deposited 2023-03-30	Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 I6H Dexverapamil × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8SB7 CryoEM structure of P-Glycoprotein in inward facing 1 state under continuous turnover conditions with verapamil Deposited 2023-04-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 I6H Dexverapamil × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8SB8 CryoEM structure of P-Glycoprotein in collapsed closed state with vanadate Deposited 2023-04-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	MG MAGNESIUM ION × 2 AOV ADP ORTHOVANADATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8SB9 CryoEM structure of P-Glycoprotein in inward facing 1 state under continuous turnover conditions with vinblastine Deposited 2023-04-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 VLB (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8SBA CryoEM structure of P-Glycoprotein in inward facing 2 state under continuous turnover conditions with vinblastine Deposited 2023-04-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 VLB (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8Y6H P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in LMNG detergent Deposited 2024-02-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	R0Z elacridar × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
8Y6I P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in nanodisc Deposited 2024-02-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1280（1280 aa）	Not recorded	CLR CHOLESTEROL × 12 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 R0Z elacridar × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
9CR8 SapNP reconstituted human ABCB1 Deposited 2024-07-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	UPL UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM HEPES (pH 7.5), 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9CTC SapNP reconstituted Human ABCB1 in complex with Zosuquidar and ATP/Mg Deposited 2024-07-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZQU Zosuquidar × 2 UPL UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID × 22	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM HEPES (pH 7.5), 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9CTF SapNP Reconstituted Human ABCB1 bound to Taxol in presence of ATP Deposited 2024-07-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	UPL UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID × 22 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 TA1 TAXOL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM HEPES (pH 7.5), 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9CTG SapNP Reconstituted Human ABCB1 bound to ATP gammaS Deposited 2024-07-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1280（1280 aa）	Not recorded	UPL UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID × 9 MG MAGNESIUM ION × 2 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM HEPES (pH 7.5), 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MDR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1280； UniProt 1–1280

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	8gmj
Deposition date deposition_date	2023-03-26
Structure title title	CryoEM structure of P-Glycoprotein in collapsed closed state under continuous turnover conditions with verapamil
Keywords keywords	multidrug resistance, ABC transporter, membrane protein, transporter, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.49 Å
Radius of gyration Rg (electron density) rg_electron	36.73 Å
Forward intensity I(0) i0	152961000.00
Molecular weight molecular_weight	80887.0 kDa
Excluded volume excluded_volume	93138 Å³
Envelope volume envelope_volume	160770 Å³
Hydration-shell volume shell_volume	39622 Å³
Envelope diameter envelope_diameter	131.3 Å
Shell Rg shell_rg	39.47 Å
Envelope Rg envelope_rg	35.96 Å
Shape Rg shape_rg	36.74 Å
Total Rg total_rg	36.89 Å
Total atoms total_atoms	7960
Residues n_residues	1145
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	124.0 Å
Rg (real space) rg_real	36.83 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	1.5300e+08
I(0) uncertainty (real space) i0_real_error	2.8550e+06
Rg (reciprocal space) rg_reciprocal	36.63 Å
I(0) (reciprocal space) i0_reciprocal	152900000.0000
Solution quality estimate total_estimate	0.8131
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.6 Å
Skewness Skewness skewness	0.552
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	54950000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.756; Smooth: 0.721

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ATP-dependent translocase ABCB1
Molecular weight formula_weight	141644.8 kDa
EC 编号 ec_number	7.6.2.2,7.6.2.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7960

MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAIIHGAGLPLMMLVFGEMTDIFANAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEIGWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFTDKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIGAAFLLIYASYALAFWYGTTLVLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFSYPSRKEVKILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLFATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENAADESKSEIDALEMSSNDSRSSLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAIINGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKAGEILTKRLRYMVFRSMLRQDVSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNIANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLSGQALKDKKELEGSGKIATEAIENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFGAYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDSYSTEGLMPNTLEGNVTFGEVVFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEPILFDCSIAENIAYGDNSRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQLLAQKGIYFSMVSVQAGTKRQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	33409

fit	/app/data/saxs_computation/gm/8gmj/8gmj.fit
pddf	/app/data/pr_computation/gm/8gmj/8gmj.pr.out
profile	/app/data/saxs_computation/gm/8gmj/8gmj.dat

CryoEM structure of P-Glycoprotein in collapsed closed state under continuous turnover conditions with verapamil

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

ATP-dependent translocase ABCB1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D