9mla

Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab

Method: ELECTRON MICROSCOPY

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

Surface protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 24	Kenv-6 Fab heavy chain × 3 Kenv-6 Fab light chain × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENK25_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–369； UniProt 97–465 Author chain B； PDBConstruct 1–369； UniProt 97–465 Author chain C； PDBConstruct 1–369； UniProt 97–465 Author chain D； PDBConstruct 1–167； UniProt 466–632 Author chain E； PDBConstruct 1–167； UniProt 466–632 Author chain F； PDBConstruct 1–167； UniProt 466–632

Transmembrane protein,Fibritin

Enterobacteria phage T4

UniProt P10104

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 24	Surface protein × 3 （P61570） Kenv-6 Fab heavy chain × 3 Kenv-6 Fab light chain × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WAC_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 186–211； UniProt 459–484 Author chain E； PDBConstruct 186–211； UniProt 459–484 Author chain F； PDBConstruct 186–211； UniProt 459–484

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	9mla
Deposition date deposition_date	2024-12-18
Structure title title	Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab
Keywords keywords	Human endogenous retrovirus K, glycoprotein, HERV-K, envelope, pre-fusion, Fab complex, VIRAL PROTEIN; VIRAL PROTEIN
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.

9mla__assembly_1__model_1

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

Download this curve (.dat)

9mla__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9mla__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.28 Å
Rg (electron density)	46.03 Å
Total Rg	46.29 Å
Atom count	18633
Residues	2223
Excluded volume	331300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9mla__assembly_1__model_1`	12-meric （12）	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	Surface protein
Molecular weight formula_weight	42193.4 kDa
Mutation mutation	V437C, S463R, K464R,
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	18633

AAANYTYWAYVPFPPLIRAVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTPRPKIISPVSGPEHPELWRLTVASHHIRIWSGNQTLETRDRKPFYTVDLNSSLTVPLQSCVKPPYMLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPCSMDRPWEASPSIHILTEVLKGVLNRRRR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	Transmembrane protein,Fibritin
Molecular weight formula_weight	27455.5 kDa
Mutation mutation	V498C
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

FIFTLIAVIMGLIAVTATAAVAGVALHSSVQSCNFVNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADGLANLNPVTWVKTDDDDKAGGSGGSGGSGGGYIPEAPRDGQAYVRKDGEWVLLSTFLASGLEVLFQGPGAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source Source

Source organism organism	Enterobacteria phage T4
Common name common_name	Bacteriophage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Drosophila melanogaster

Entity 3 Entity 3 polymer

Description description	Kenv-6 Fab heavy chain
Molecular weight formula_weight	13437.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

QIQLVQSGPELKKPGETVKISCKASGYTFTIYGMNWLKQAPGKGLKWMGWINTYTGEPTYADDFKGRFAFSLETSASTAYLQVNNLKNEDTATYFCAKYYDGYYGWYFDVWGAGTTLTV

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	Kenv-6 Fab light chain
Molecular weight formula_weight	11671.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L

IVLTQSPASLAVTLGQRATISCRGSESVDSYGNSFMHWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSYEDPYTFGGGTKL

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Cricetulus griseus

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	12

Entity 7 Entity 7 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	6

Entity 8 Entity 8 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

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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	2.24 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	479625

Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab

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

Surface protein

State in the Current Structure

Other States of the Same Protein in the Database

Transmembrane protein,Fibritin

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9mla__assembly_1__model_1

9mla__assembly_1__model_1 | I(q)

9mla__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

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

7. Citations (1)

Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab

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

Surface protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transmembrane protein,Fibritin

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

9mla__assembly_1__model_1

9mla__assembly_1__model_1 | I(q)

9mla__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

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

7. Citations (1)