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6dlw

Complement component polyC9

Method: ELECTRON MICROSCOPY Dmax: 246.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Complement component C9

Homo sapiens

UniProt P02748

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 homooligomer Homooligomer Protein × 22 PDB declaration: 22-meric（22） Consistent with protein copy count Chain A； UniProt 22–559 Chain B； UniProt 22–559 Chain C； UniProt 22–559 Chain D； UniProt 22–559 Chain E； UniProt 22–559 Chain F； UniProt 22–559 Chain G； UniProt 22–559 Chain H； UniProt 22–559 Chain I； UniProt 22–559 Chain J； UniProt 22–559 Chain K； UniProt 22–559 Chain L； UniProt 22–559 Chain M； UniProt 22–559 Chain N； UniProt 22–559 Chain O； UniProt 22–559 Chain P； UniProt 22–559 Chain Q； UniProt 22–559 Chain R； UniProt 22–559 Chain S； UniProt 22–559 Chain T； UniProt 22–559 Chain U； UniProt 22–559 Chain V； UniProt 22–559 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 BMA beta-D-mannopyranose × 22 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 2 seconds before plunging Resolution 3.90 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 6DLW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FMW The poly-C9 component of the Complement Membrane Attack Complex Deposited 2015-11-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 22 PDB declaration: 22-meric
Chain A 39–544（506 aa）
Chain B 39–544（506 aa）
Chain C 39–544（506 aa）
Chain D 39–544（506 aa）
Chain E 39–544（506 aa）
Chain F 39–544（506 aa）
Chain G 39–544（506 aa）
Chain H 39–544（506 aa）
Chain I 39–544（506 aa）
Chain J 39–544（506 aa）
Chain K 39–544（506 aa）
Chain L 39–544（506 aa）
Chain M 39–544（506 aa）
Chain N 39–544（506 aa）
Chain O 39–544（506 aa）
Chain P 39–544（506 aa）
Chain Q 39–544（506 aa）
Chain R 39–544（506 aa）
Chain S 39–544（506 aa）
Chain T 39–544（506 aa）
Chain U 39–544（506 aa）
Chain V 39–544（506 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 MM TRIS, 50 MM NACL；pH 8；10 MM TRIS, 50 MM NACL
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 6.70 Å
6H03 OPEN CONFORMATION OF THE MEMBRANE ATTACK COMPLEX Deposited 2018-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric
Chain G 22–559（538 aa）
Chain H 22–559（538 aa）
Chain I 22–559（538 aa）
Chain J 22–559（538 aa）
Chain K 22–559（538 aa）
Chain L 22–559（538 aa）
Chain M 22–559（538 aa）
Chain N 22–559（538 aa）
Chain O 22–559（538 aa）
Chain P 22–559（538 aa）
Chain Q 22–559（538 aa）
Chain R 22–559（538 aa）
Chain S 22–559（538 aa）
Chain T 22–559（538 aa）
Chain U 22–559（538 aa）
Chain V 22–559（538 aa）
Chain W 22–559（538 aa）
Chain X 22–559（538 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6H04 Closed conformation of the Membrane Attack Complex Deposited 2018-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric
Chain G 22–559（538 aa）
Chain H 22–559（538 aa）
Chain I 22–559（538 aa）
Chain J 22–559（538 aa）
Chain K 22–559（538 aa）
Chain L 22–559（538 aa）
Chain M 22–559（538 aa）
Chain N 22–559（538 aa）
Chain O 22–559（538 aa）
Chain P 22–559（538 aa）
Chain Q 22–559（538 aa）
Chain R 22–559（538 aa）
Chain S 22–559（538 aa）
Chain T 22–559（538 aa）
Chain U 22–559（538 aa）
Chain V 22–559（538 aa）
Chain W 22–559（538 aa）
Chain X 22–559（538 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
7NYC cryoEM structure of 3C9-sMAC Deposited 2021-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 22–559（538 aa）
Chain H 22–559（538 aa）
Chain I 22–559（538 aa）
Not recorded MAN alpha-D-mannopyranose × 7 CA CALCIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FUC alpha-L-fucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7NYD cryoEM structure of 2C9-sMAC Deposited 2021-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain G 22–559（538 aa）
Chain H 22–559（538 aa）
Not recorded MAN alpha-D-mannopyranose × 6 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FUC alpha-L-fucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8B0G 2C9, C5b9-CD59 structure Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–559（559 aa）
Chain I 1–559（559 aa）
Chain J 1–559（559 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 120 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8B0H 2C9, C5b9-CD59 cryoEM structure Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–559（559 aa）
Chain I 1–559（559 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 120 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8DE6 Oligomeric C9 in complex with aE11 Fab Deposited 2022-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 21–559（539 aa）
Chain C 21–559（539 aa）
Chain G 21–559（539 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 BMA beta-D-mannopyranose × 6 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CO9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–538； UniProt 22–559 Author chain B； PDBConstruct 1–538； UniProt 22–559 Author chain C； PDBConstruct 1–538； UniProt 22–559 Author chain D； PDBConstruct 1–538； UniProt 22–559 Author chain E； PDBConstruct 1–538； UniProt 22–559 Author chain F； PDBConstruct 1–538； UniProt 22–559 Author chain G； PDBConstruct 1–538； UniProt 22–559 Author chain H； PDBConstruct 1–538； UniProt 22–559 Author chain I； PDBConstruct 1–538； UniProt 22–559 Author chain J； PDBConstruct 1–538； UniProt 22–559 Author chain K； PDBConstruct 1–538； UniProt 22–559 Author chain L； PDBConstruct 1–538； UniProt 22–559 Author chain M； PDBConstruct 1–538； UniProt 22–559 Author chain N； PDBConstruct 1–538； UniProt 22–559 Author chain O； PDBConstruct 1–538； UniProt 22–559 Author chain P； PDBConstruct 1–538； UniProt 22–559 Author chain Q； PDBConstruct 1–538； UniProt 22–559 Author chain R； PDBConstruct 1–538； UniProt 22–559 Author chain S； PDBConstruct 1–538； UniProt 22–559 Author chain T； PDBConstruct 1–538； UniProt 22–559 Author chain U； PDBConstruct 1–538； UniProt 22–559 Author chain V； PDBConstruct 1–538； UniProt 22–559

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 6dlw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dlw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dlw
Deposition date deposition_date2018-06-03
Structure title titleComplement component polyC9
Keywords keywordsComplement, pore, EM, membrane, transmembrane, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier94.83 Å
Radius of gyration Rg (electron density) rg_electron93.15 Å
Forward intensity I(0) i019472800000.00
Molecular weight molecular_weight1148000.0 kDa
Excluded volume excluded_volume1418700 ų
Envelope volume envelope_volume3181200 ų
Hydration-shell volume shell_volume279100 ų
Envelope diameter envelope_diameter246.5 Å
Shell Rg shell_rg105.70 Å
Envelope Rg envelope_rg83.40 Å
Shape Rg shape_rg93.12 Å
Total Rg total_rg93.38 Å
Total atoms total_atoms80410
Residues n_residues10120
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 dmax246.7 Å
Rg (real space) rg_real93.83 Å
Rg uncertainty (real space) rg_real_error0.84 Å
I(0) (real space) i0_real1.9450e+10
I(0) uncertainty (real space) i0_real_error4.0330e+08
Rg (reciprocal space) rg_reciprocal97.54 Å
I(0) (reciprocal space) i0_reciprocal19650000000.0000
Solution quality estimate total_estimate0.8248
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary154.2 Å
Skewness Skewness skewness-0.291
Kurtosis Kurtosis kurtosis-0.877
Angular range angular_range— – 0.0800 Å−1
Current regularization parameter α current_alpha0.0456
Highest regularization parameter α highest_alpha529500000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)