SAXSdb — 6nip

▼

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

Envelope protein E

Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	MZ1 Heavy chain × 2 MZ1 Light Chain × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_ZIKVF
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–405； UniProt 291–695 Author chain Z； PDBConstruct 1–405； UniProt 291–695

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nip
Deposition date deposition_date	2018-12-31
Structure title title	Crystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ1 in complex with ZIKV E glycoprotein
Keywords keywords	ZIKV-DENV, Antibody, human, Vaccination, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6nip__assembly_1__model_1

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

Download this curve (.dat)

6nip__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nip__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	70.13 Å
Rg (electron density)	71.83 Å
Total Rg	71.26 Å
Atom count	12608
Residues	1668
Excluded volume	223090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nip__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MZ1 Heavy chain
Molecular weight formula_weight	23927.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	12632

QVQLQESGPGLVKSSETLSLSCTVSGASISNFYWSWVRQPPGKGLEWMGSIYYTGTITYNPSLKSRLTMSVDTSKNQFSLKLNSVTAADTAVYSCAGLDRFNWNDEGDCWGQGTLVTVFSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	MZ1 Light Chain
Molecular weight formula_weight	22981.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QSVLTQPPSASGTPGQRVTISCSGSRSNLGRNTVNWYQQLPGVAPKLLIYSNNRRPSGVPDRFSGSKSDTSASLAISGLQSEDEADYFCAAWDDSLNGLYVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope protein E
Molecular weight formula_weight	48397.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,E

IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSGPLEVLFQGPGSAWSHPQFEKGGGSGGGSGGGSAWSHPQFEK

Source Source

Source organism organism	Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	2043570
Host organism host_organism	Drosophila melanogaster

▶

Unit-cell length a length_a	417.330 Å
Unit-cell length b length_b	69.300 Å
Unit-cell length c length_c	212.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	4.160 Å
Low-resolution limit resolution_low	14.987 Å
R factor r_factor	0.1901
R_work r_work	0.1876
R_free r_free	0.2366

Crystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ1 in complex with ZIKV E glycoprotein

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

Envelope protein E

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

6nip__assembly_1__model_1

6nip__assembly_1__model_1 | I(q)

6nip__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)

Crystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ1 in complex with ZIKV E glycoprotein

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

Envelope protein E

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

6nip__assembly_1__model_1

6nip__assembly_1__model_1 | I(q)

6nip__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)