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6y4l

Crystal structure of human ER membrane protein complex subunits EMC2 and EMC9

Method: X-RAY DIFFRACTION Dmax: 83.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ER membrane protein complex subunit 2

Homo sapiens

UniProt Q15006

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 11–274 Not recorded ER membrane protein complex subunit 9 × 1 （Q9Y3B6） SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；293.15 K；34% PEG4000, 0.1 M Tris pH 8.3, and 0.2 M lithium sulfate (For I03 native dataset) X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；293.15 K；28% PEG4000, 0.1 M Tris pH 8.3, and 0.2 M lithium sulfate (For I23 S-SAD dataset) Resolution 2.20 Å R-free 0.250

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 6Y4L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WW7 Structure of the human ER membrane protein complex in a lipid nanodisc Deposited 2020-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–297（297 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z3W Human ER membrane protein complex Deposited 2020-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7ADO Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs Deposited 2020-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–297（297 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 6；10 mM ammonium citrate pH 6.0, 100 mM sodium chloride, 0.25 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
7ADP Cryo-EM structure of human ER membrane protein complex in GDN detergent Deposited 2020-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–297（297 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 6；10 mM ammonium citrate pH 6.0, 100 mM sodium chloride, 0.25 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8EOI Structure of a human EMC:human Cav1.2 channel complex in GDN detergent Deposited 2022-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 3–293（291 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8J0N cryo-EM structure of human EMC Deposited 2023-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8J0O cryo-EM structure of human EMC and VDAC Deposited 2023-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8S9S Structure of the human ER membrane protein complex (EMC) in GDN Deposited 2023-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain 2 1–297（297 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9C7V Structure of the human BOS:human EMC complex in GDN Deposited 2024-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain 2 1–297（297 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
9ZZ6 The ER membrane protein complex acts as a chaperone to promote voltage-gated calcium channel assembly Deposited 2026-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–297（297 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；pH 7.5 adjusted with KOH ( potassium hydroxide).
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EMC2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–265； UniProt 11–274

ER membrane protein complex subunit 9

Homo sapiens

UniProt Q9Y3B6

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–200 Not recorded ER membrane protein complex subunit 2 × 1 （Q15006） SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；293.15 K；34% PEG4000, 0.1 M Tris pH 8.3, and 0.2 M lithium sulfate (For I03 native dataset) X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；293.15 K；28% PEG4000, 0.1 M Tris pH 8.3, and 0.2 M lithium sulfate (For I23 S-SAD dataset) Resolution 2.20 Å R-free 0.250

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 6Y4L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6Z3W Human ER membrane protein complex Deposited 2020-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–208（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EMC9_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–200； UniProt 1–200

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 6y4l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y4l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y4l
Deposition date deposition_date2020-02-21
Structure title titleCrystal structure of human ER membrane protein complex subunits EMC2 and EMC9
Keywords keywordsComplex, insertase, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.29 Å
Radius of gyration Rg (electron density) rg_electron24.40 Å
Forward intensity I(0) i042765600.00
Molecular weight molecular_weight50040.0 kDa
Excluded volume excluded_volume62286 ų
Envelope volume envelope_volume77438 ų
Hydration-shell volume shell_volume26749 ų
Envelope diameter envelope_diameter88.1 Å
Shell Rg shell_rg31.29 Å
Envelope Rg envelope_rg24.24 Å
Shape Rg shape_rg24.40 Å
Total Rg total_rg25.16 Å
Total atoms total_atoms3518
Residues n_residues456
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 dmax83.5 Å
Rg (real space) rg_real25.22 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real4.2770e+07
I(0) uncertainty (real space) i0_real_error6.2710e+05
Rg (reciprocal space) rg_reciprocal25.24 Å
I(0) (reciprocal space) i0_reciprocal42770000.0000
Solution quality estimate total_estimate0.8944
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.5 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.374
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6386000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)