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2n7q

Structure of the transmembrane domain of human nicastrin in SDS micelles

Method: SOLUTION NMR Dmax: 72.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nicastrin

Homo sapiens

UniProt Q92542

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 664–709 Fragment：UNP residues 664-709 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；313 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition：0.8 mM [U-100% 13C; U-100% 15N] transmembrane domain of human nicastrin-1, 20 mM sodium phosphate-2, 100 mM SDS-3, 1 mM DTT-4, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2N7Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N7R Structure of the transmembrane domain of human nicastrin in DPC micelles Deposited 2015-09-17 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 664–709（46 aa） Fragment：UNP residues 664-709
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；313 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] transmembrane domain of human nicastrin-1, 20 mM sodium phosphate-2, 200 mM DPC-3, 1 mM DTT-4, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5A63 Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution. Deposited 2015-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35；pH 7.4；25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 85, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 4 SECONDS BEFORE PLUNGING,
Resolution 3.40 Å
5FN2 Cryo-EM structure of gamma secretase in complex with a drug DAPT Deposited 2015-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35；pH 7.4；25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 4.20 Å
5FN3 Cryo-EM structure of gamma secretase in class 1 of the apo- state ensemble Deposited 2015-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35；pH 7.4；25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 4.10 Å
5FN4 Cryo-EM structure of gamma secretase in class 2 of the apo- state ensemble Deposited 2015-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35；pH 7.4；25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 4.00 Å
5FN5 Cryo-EM structure of gamma secretase in class 3 of the apo- state ensemble Deposited 2015-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35；pH 7.4；25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 4.30 Å
6IDF Cryo-EM structure of gamma secretase in complex with a Notch fragment Deposited 2018-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6IYC Recognition of the Amyloid Precursor Protein by Human gamma-secretase Deposited 2018-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6LQG Human gamma-secretase in complex with small molecule Avagacestat Deposited 2020-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EN9 (2R)-2-[(4-chlorophenyl)sulfonyl-[[2-fluoranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]methyl]amino]-5,5,5-tris(fluoranyl)pentanamide × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6LR4 Molecular basis for inhibition of human gamma-secretase by small molecule Deposited 2020-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ESF (2S)-2-hydroxy-3-methyl-N-[(2S)-1-[[(5S)-3-methyl-4-oxo-2,5-dihydro-1H-3-benzazepin-5-yl]amino]-1-oxopropan-2-yl]butanamide × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7C9I Human gamma-secretase in complex with small molecule L-685,458 Deposited 2020-06-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 FTO ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7D8X CryoEM structure of human gamma-secretase in complex with E2012 and L685458 Deposited 2020-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 GZR 1-[(1S)-1-(4-fluorophenyl)ethyl]-3-[[3-methoxy-4-(4-methylimidazol-1-yl)phenyl]methylidene]piperidin-2-one × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1 FTO ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7Y5T CryoEM structure of PS1-containing gamma-secretase in complex with MRK-560 Deposited 2022-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 IGD ~{N}-[4-[2,5-bis(fluoranyl)phenyl]-4-(4-chlorophenyl)sulfonyl-cyclohexyl]-1,1,1-tris(fluoranyl)methanesulfonamide × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7Y5X CryoEM structure of PS2-containing gamma-secretase treated with MRK-560 Deposited 2022-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Y5Z CryoEM structure of human PS2-containing gamma-secretase Deposited 2022-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8IM7 Human gamma-secretase treated with ganglioside GM1 Deposited 2023-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8K8E Human gamma-secretase in complex with a substrate mimetic Deposited 2023-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8KCO Cryo-EM structure of human gamma-secretase in complex with RO4929097 Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–701（701 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 N60 2,2-dimethyl-N-[(7S)-6-oxo-5,7-dihydrobenzo[d][1]benzazepin-7-yl]-N'-(2,2,3,3,3-pentafluoropropyl)propanediamide × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KCP Cryo-EM structure of human gamma-secretase in complex with Crenigacestat Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–701（701 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 N9C 4,4,4-tris(fluoranyl)-N-[(2S)-1-[[(7S)-5-(2-hydroxyethyl)-6-oxidanylidene-7H-pyrido[2,3-d][3]benzazepin-7-yl]amino]-1-oxidanylidene-propan-2-yl]butanamide × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8KCS Cryo-EM structure of human gamma-secretase in complex with BMS906024 Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–701（701 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 Q70 Osugacestat × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8KCT Cryo-EM structure of human gamma-secretase in complex with Nirogacestat Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–701（701 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CLR CHOLESTEROL × 3 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 O6U Nirogacestat × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8KCU Cryo-EM structure of human gamma-secretase in complex with MK-0752 Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–701（701 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 OL9 MK-0752 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8OQY Structure of apo form of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc Deposited 2023-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OQZ Structure of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc in complex with Ab46 Deposited 2023-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8X52 Cryo-EM structure of human gamma-secretase in complex with Abeta49 Deposited 2023-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8X53 Cryo-EM structure of human gamma-secretase in complex with Abeta46 Deposited 2023-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8X54 Cryo-EM structure of human gamma-secretase in complex with APP-C99 Deposited 2023-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9K95 Cryo-EM structure of human gamma-secretase in complex with compound E Deposited 2024-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–709（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 A1D6X (2~{S})-2-[2-[3,5-bis(fluoranyl)phenyl]ethanoylamino]-~{N}-[(3~{S})-1-methyl-2-oxidanylidene-5-phenyl-3~{H}-1,4-benzodiazepin-3-yl]propanamide × 1 CLR CHOLESTEROL × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NICA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–54； UniProt 664–709

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2n7q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2n7q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2n7q
Deposition date deposition_date2015-09-17
Structure title titleStructure of the transmembrane domain of human nicastrin in SDS micelles
Keywords keywordsDetergent micelles, gamma-secretase, nicastrin, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.79 Å
Radius of gyration Rg (electron density) rg_electron18.24 Å
Forward intensity I(0) i0104285000.00
Molecular weight molecular_weight99138.0 kDa
Excluded volume excluded_volume129670 ų
Envelope volume envelope_volume24993 ų
Hydration-shell volume shell_volume11070 ų
Envelope diameter envelope_diameter76.3 Å
Shell Rg shell_rg25.44 Å
Envelope Rg envelope_rg22.12 Å
Shape Rg shape_rg18.21 Å
Total Rg total_rg18.63 Å
Total atoms total_atoms14380
Residues n_residues920
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax72.9 Å
Rg (real space) rg_real18.34 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real1.0430e+08
I(0) uncertainty (real space) i0_real_error1.5630e+06
Rg (reciprocal space) rg_reciprocal18.28 Å
I(0) (reciprocal space) i0_reciprocal104300000.0000
Solution quality estimate total_estimate0.6177
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary4.9 Å
Skewness Skewness skewness0.524
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.4450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11360.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.001; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.024; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)