8d4e

Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes

Method: ELECTRON MICROSCOPY

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

ADP-ribosylation factor 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Protein Nef × 2 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） AP-1 complex subunit beta-1 × 1 （Q10567） AP-1 complex subunit gamma-1 × 1 （P22892） AP-1 complex subunit mu-1 × 1 （P35585） AP-1 complex subunit sigma-3 × 1 （Q96PC3） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–180； UniProt 2–181 Author chain H； PDBConstruct 1–180； UniProt 2–181 Author chain Z； PDBConstruct 1–180； UniProt 2–181

Protein Nef

Human immunodeficiency virus 1

UniProt Q90VU7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ADP-ribosylation factor 1 × 3 （P84077） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） AP-1 complex subunit beta-1 × 1 （Q10567） AP-1 complex subunit gamma-1 × 1 （P22892） AP-1 complex subunit mu-1 × 1 （P35585） AP-1 complex subunit sigma-3 × 1 （Q96PC3） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q90VU7_9HIV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–205； UniProt 2–206 Author chain N； PDBConstruct 1–205； UniProt 2–206

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ADP-ribosylation factor 1 × 3 （P84077） Protein Nef × 2 （Q90VU7） AP-1 complex subunit beta-1 × 1 （Q10567） AP-1 complex subunit gamma-1 × 1 （P22892） AP-1 complex subunit mu-1 × 1 （P35585） AP-1 complex subunit sigma-3 × 1 （Q96PC3） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLAA_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Y； PDBConstruct 2–33； UniProt 334–365

AP-1 complex subunit beta-1

Homo sapiens

UniProt Q10567

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ADP-ribosylation factor 1 × 3 （P84077） Protein Nef × 2 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） AP-1 complex subunit gamma-1 × 1 （P22892） AP-1 complex subunit mu-1 × 1 （P35585） AP-1 complex subunit sigma-3 × 1 （Q96PC3） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP1B1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–949； UniProt 1–949

AP-1 complex subunit gamma-1

Mus musculus

UniProt P22892

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ADP-ribosylation factor 1 × 3 （P84077） Protein Nef × 2 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） AP-1 complex subunit beta-1 × 1 （Q10567） AP-1 complex subunit mu-1 × 1 （P35585） AP-1 complex subunit sigma-3 × 1 （Q96PC3） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP1G1_MOUSE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain G； PDBConstruct 1–595； UniProt 1–595

AP-1 complex subunit mu-1

Mus musculus

UniProt P35585

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ADP-ribosylation factor 1 × 3 （P84077） Protein Nef × 2 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） AP-1 complex subunit beta-1 × 1 （Q10567） AP-1 complex subunit gamma-1 × 1 （P22892） AP-1 complex subunit sigma-3 × 1 （Q96PC3） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP1M1_MOUSE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–422； UniProt 2–423

AP-1 complex subunit sigma-3

Homo sapiens

UniProt Q96PC3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ADP-ribosylation factor 1 × 3 （P84077） Protein Nef × 2 （Q90VU7） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） AP-1 complex subunit beta-1 × 1 （Q10567） AP-1 complex subunit gamma-1 × 1 （P22892） AP-1 complex subunit mu-1 × 1 （P35585） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP1S3_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain S； PDBConstruct 1–154； UniProt 1–154

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	8d4e
Deposition date deposition_date	2022-06-01
Structure title title	Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes
Keywords keywords	nef, AP, trafficking, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8d4e__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8d4e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8d4e__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	47.80 Å
Rg (electron density)	47.49 Å
Total Rg	47.63 Å
Atom count	9767
Residues	2417
Excluded volume	134450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8d4e__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	ADP-ribosylation factor 1
Molecular weight formula_weight	20590.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H,Z
Atom count atom_count	9767

GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Protein Nef
Molecular weight formula_weight	24154.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,L

GGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNCGHHHHHH

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	HLA class I histocompatibility antigen, A alpha chain
Molecular weight formula_weight	4139.4 kDa
Mutation mutation	T345S, S349G, G355S, C363A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

CRKSSDRKGGSYSQAAGSDSAQSSDVSLTAAKVHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	AP-1 complex subunit beta-1
Molecular weight formula_weight	104736.5 kDa
Mutation mutation	K359R, E476K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELREYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQVQLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEVVLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEGGRGVVHKSLPPRTASSESAESPETAPTGAPPGEQPDVIPAQGDLLGDLLNLDLGPPVSGPPLATSSVQMGAVDLLGGGLDSLMGDEPEGIGGTNFVAPPTAAVPANLGAPIGSGLSDLFDLTSGVGTLSGSYVAPKAVWLPAMKAKGLEISGTFTRQVGSISMDLQLTNKALQVMTDFAIQFNRNSFGLAPAAPLQVHAPLSPNQTVEISLPLSTVGSVMKMEPLNNLQVAVKNNIDVFYFSTLYPLHILFVEDGKMDRQMFLATWKDIPNENEAQFQIRDCPLNAEAASSKLQSSNIFTVAKRNVEGQDMLYQSLKLTNGIWVLAELRIQPGNPSCTDLELSLKCRAPEVSQHVYQAYETILKN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	AP-1 complex subunit gamma-1
Molecular weight formula_weight	68194.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLGYPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQGLALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATKNLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGISDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIKSESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHIDTIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCIGEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCTVNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYFQ

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	AP-1 complex subunit mu-1
Molecular weight formula_weight	48475.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTQ

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 polymer

Description description	AP-1 complex subunit sigma-3
Molecular weight formula_weight	18305.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYKRYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEIQETSKKIAVKAIEDSDMLQEVSTVSQTMGER

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 8 Entity 8 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

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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	triclinic

Resolution resolution	9.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	18183

Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes

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

ADP-ribosylation factor 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein Nef

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HLA class I histocompatibility antigen, A alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-1 complex subunit beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-1 complex subunit gamma-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-1 complex subunit mu-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-1 complex subunit sigma-3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8d4e__assembly_1__model_1

8d4e__assembly_1__model_1 | I(q)

8d4e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source