SAXSdb — 7d5z

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

Envelope glycoprotein H

Human gammaherpesvirus 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein L × 1 （Q3KSS3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein L × 1 （Q3KSS3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein L × 1 （Q3KSS3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein L × 1 （Q3KSS3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GH_EBVG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–660； UniProt 20–679 Author chain E； PDBConstruct 1–660； UniProt 20–679 Author chain I； PDBConstruct 1–660； UniProt 20–679 Author chain M； PDBConstruct 1–660； UniProt 20–679

Envelope glycoprotein L

Human gammaherpesvirus 4

UniProt Q3KSS3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein H × 1 （Q3KSQ3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein H × 1 （Q3KSQ3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein H × 1 （Q3KSQ3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein H × 1 （Q3KSQ3） light chain of 1D8 × 1 heavy chain of 1D8 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GL_EBVG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–112； UniProt 24–135 Author chain F； PDBConstruct 1–112； UniProt 24–135 Author chain J； PDBConstruct 1–112； UniProt 24–135 Author chain N； PDBConstruct 1–112； UniProt 24–135

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	7d5z
Deposition date deposition_date	2020-09-28
Structure title title	Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8
Keywords keywords	EBV gH/gL, antibody, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

7d5z__assembly_1__model_1

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

Download this curve (.dat)

7d5z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d5z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.88 Å
Rg (electron density)	40.90 Å
Total Rg	41.00 Å
Atom count	9076
Residues	1176
Excluded volume	162180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d5z__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7d5z__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7d5z__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7d5z__assembly_4__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	73959.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,A,E,I
Atom count atom_count	36304

LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLIFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEAMLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLYEERAHHHHHH

Source Source

Source organism organism	Human gammaherpesvirus 4
Common name common_name	HHV-4
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	12491.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,B,F,J

WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTSHLRELLTTLESLYGSFSVEDLFGANLNRYAWHR

Source Source

Source organism organism	Human gammaherpesvirus 4
Common name common_name	HHV-4
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	light chain of 1D8
Molecular weight formula_weight	25496.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,C,G,K

MGWSCIILFLVATATGVHSDIVMTQTPPSLSASVGDRVTLTCRASQAIRNNLAWYQHKPGKAPKRLIYAASTLEDGVPSSFSGSGFGTDFTLTINSLQPEDFATYYCLQHSTYPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

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

Entity 4 Entity 4 polymer

Description description	heavy chain of 1D8
Molecular weight formula_weight	51550.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,D,H,L

MGWSCIILFLVATATGVHSEVQLVESGGRVVQPGGSLRLSCVTSGFTFSYYPIHWVRQGPGKGLEWVTMMSFDGTSDHCISSVKGRFVMSRDNSRNTLYLEMNKMRLEDTGVYYCARGGWKWPGGAFDVFGPGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Source Source

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

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Unit-cell length a length_a	212.865 Å
Unit-cell length b length_b	212.865 Å
Unit-cell length c length_c	598.128 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	50.030 Å
R factor r_factor	0.2474
R_work r_work	0.2458
R_free r_free	0.2774

Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8

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

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein L

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

7d5z__assembly_1__model_1

7d5z__assembly_1__model_1 | I(q)

7d5z__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 (4)

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

7. Citations (1)

Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8

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

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein L

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

7d5z__assembly_1__model_1

7d5z__assembly_1__model_1 | I(q)

7d5z__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 (4)

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

7. Citations (1)