8JL4 | pdb_00008jl4

membrane proteins

PDB DOI: https://doi.org/10.2210/pdb8JL4/pdb
EM Map EMD-36388: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-06-02 Released: 2024-05-22
Deposition Author(s): Yu, J., Ge, J.P., Xu, R.S.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8JL4

This is version 1.2 of the entry. See complete history.

Literature

membrane proteins

Yu, J., Ge, J.P., Xu, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 170.73 kDa
Atom Count: 9,588
Modeled Residue Count: 1,066
Deposited Residue Count: 1,412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparan-alpha-glucosaminide N-acetyltransferase	A, B	706	Homo sapiens	Mutation(s): 0 Gene Names: HGSNAT, TMEM76 EC: 2.3.1.78 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q68CP4 (Homo sapiens) Explore Q68CP4 Go to UniProtKB: Q68CP4
PHAROS: Q68CP4 GTEx: ENSG00000165102
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q68CP4
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q68CP4-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain VA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain VA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain VA [auth B]	H [auth A], VA [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain H [auth A] Focus chain VA [auth B] Interactions & Density Focus chain H [auth A] Focus chain VA [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain EB [auth B] SDF format, chain GA [auth A] SDF format, chain Q [auth A] SDF format, chain UB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain UB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain UB [auth B]	EB [auth B], GA [auth A], Q [auth A], UB [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain EB [auth B] Focus chain GA [auth A] Focus chain Q [auth A] Focus chain UB [auth B] Interactions & Density Focus chain EB [auth B] Focus chain GA [auth A] Focus chain Q [auth A] Focus chain UB [auth B]
UV6 (Subject of Investigation/LOI) Query on UV6 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain UA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain UA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain UA [auth B]	G [auth A], UA [auth B]	~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-[[(2~{R},4~{R})-4-methyl-2-oxidanyl-3,4-dihydro-2~{H}-chromen-7-yl]oxy]-4,5-bis(oxidanyl)oxan-3-yl]ethanamide C₁₈ H₂₅ N O₈ STEBYXKOKBUTKJ-ZAIAHUIPSA-N		Interactions Focus chain G [auth A] Focus chain UA [auth B] Interactions & Density Focus chain G [auth A] Focus chain UA [auth B]
R16 Query on R16 Download:Ideal Coordinates CCD File SDF format, chain AC [auth B] SDF format, chain MA [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain MA [auth A] mmCIF format, chain AC [auth B] mmCIF format, chain MA [auth A]	AC [auth B], MA [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AC [auth B] Focus chain MA [auth A] Interactions & Density Focus chain AC [auth B] Focus chain MA [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain WA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain WA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain WA [auth B]	I [auth A], WA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain WA [auth B] Interactions & Density Focus chain I [auth A] Focus chain WA [auth B]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain CB [auth B] SDF format, chain EA [auth A] SDF format, chain GB [auth B] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain OB [auth B] SDF format, chain S [auth A] SDF format, chain SB [auth B] SDF format, chain T [auth A] SDF format, chain VB [auth B] SDF format, chain WB [auth B] SDF format, chain XA [auth B] SDF format, chain XB [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain WB [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SB [auth B] mmCIF format, chain T [auth A] mmCIF format, chain VB [auth B] mmCIF format, chain WB [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B]	AA [auth A] AB [auth B] CB [auth B] EA [auth A] GB [auth B] AA [auth A], AB [auth B], CB [auth B], EA [auth A], GB [auth B], HA [auth A], HB [auth B], IA [auth A], J [auth A], JA [auth A], K [auth A], L [auth A], M [auth A], O [auth A], OB [auth B], S [auth A], SB [auth B], T [auth A], VB [auth B], WB [auth B], XA [auth B], XB [auth B], YA [auth B], ZA [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain CB [auth B] Focus chain EA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain OB [auth B] Focus chain S [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain XA [auth B] Focus chain XB [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain CB [auth B] Focus chain EA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain OB [auth B] Focus chain S [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain XA [auth B] Focus chain XB [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain KB [auth B] SDF format, chain SA [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth B] SDF format, chain W [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain W [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain TB [auth B] mmCIF format, chain W [auth A]	FA [auth A] KB [auth B] SA [auth A] TA [auth B] TB [auth B] FA [auth A], KB [auth B], SA [auth A], TA [auth B], TB [auth B], W [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain KB [auth B] Focus chain SA [auth A] Focus chain TA [auth B] Focus chain TB [auth B] Focus chain W [auth A] Interactions & Density Focus chain FA [auth A] Focus chain KB [auth B] Focus chain SA [auth A] Focus chain TA [auth B] Focus chain TB [auth B] Focus chain W [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain JB [auth B] SDF format, chain V [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain V [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain V [auth A]	JB [auth B], V [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain JB [auth B] Focus chain V [auth A] Interactions & Density Focus chain JB [auth B] Focus chain V [auth A]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain BC [auth B] SDF format, chain CA [auth A] SDF format, chain CC [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain DC [auth B] SDF format, chain EC [auth B] SDF format, chain FB [auth B] SDF format, chain FC [auth B] SDF format, chain IB [auth B] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth B] SDF format, chain OA [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain U [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YB [auth B] SDF format, chain Z [auth A] SDF format, chain ZB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth B] MOL2 format, chain EC [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain BC [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CC [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain DC [auth B] mmCIF format, chain EC [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain FC [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth B] mmCIF format, chain U [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth B]	BB [auth B] BC [auth B] CA [auth A] CC [auth B] DA [auth A] BB [auth B], BC [auth B], CA [auth A], CC [auth B], DA [auth A], DB [auth B], DC [auth B], EC [auth B], FB [auth B], FC [auth B], IB [auth B], KA [auth A], LA [auth A], LB [auth B], MB [auth B], N [auth A], NA [auth A], NB [auth B], OA [auth A], P [auth A], PA [auth A], QA [auth A], QB [auth B], R [auth A], RA [auth A], RB [auth B], U [auth A], X [auth A], Y [auth A], YB [auth B], Z [auth A], ZB [auth B]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain BB [auth B] Focus chain BC [auth B] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth B] Focus chain EC [auth B] Focus chain FB [auth B] Focus chain FC [auth B] Focus chain IB [auth B] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain U [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZB [auth B] Interactions & Density Focus chain BB [auth B] Focus chain BC [auth B] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth B] Focus chain EC [auth B] Focus chain FB [auth B] Focus chain FC [auth B] Focus chain IB [auth B] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain U [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZB [auth B]
HP6 Query on HP6 Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain PB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain PB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain PB [auth B]	BA [auth A], PB [auth B]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain PB [auth B] Interactions & Density Focus chain BA [auth A] Focus chain PB [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Structure summary
Version 1.2: 2025-07-02
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.