3tcx

Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation

Method: X-RAY DIFFRACTION

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

Intercellular adhesion molecule 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 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
13	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
14	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-L × 1 （P20701） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ICAM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–85； UniProt 29–112 Author chain C； PDBConstruct 3–85； UniProt 29–112 Author chain E； PDBConstruct 3–85； UniProt 29–112 Author chain G； PDBConstruct 3–85； UniProt 29–112 Author chain I； PDBConstruct 3–85； UniProt 29–112 Author chain K； PDBConstruct 3–85； UniProt 29–112 Author chain M； PDBConstruct 3–85； UniProt 29–112 Author chain O； PDBConstruct 3–85； UniProt 29–112 Author chain Q； PDBConstruct 3–85； UniProt 29–112 Author chain S； PDBConstruct 3–85； UniProt 29–112 Author chain U； PDBConstruct 3–85； UniProt 29–112 Author chain W； PDBConstruct 3–85； UniProt 29–112 Author chain Y； PDBConstruct 3–85； UniProt 29–112 Author chain a； PDBConstruct 3–85； UniProt 29–112

Integrin alpha-L

Homo sapiens

UniProt P20701

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
13	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
14	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Intercellular adhesion molecule 1 × 1 （P05362） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITAL_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–180； UniProt 154–332 Author chain D； PDBConstruct 2–180； UniProt 154–332 Author chain F； PDBConstruct 2–180； UniProt 154–332 Author chain H； PDBConstruct 2–180； UniProt 154–332 Author chain J； PDBConstruct 2–180； UniProt 154–332 Author chain L； PDBConstruct 2–180； UniProt 154–332 Author chain N； PDBConstruct 2–180； UniProt 154–332 Author chain P； PDBConstruct 2–180； UniProt 154–332 Author chain R； PDBConstruct 2–180； UniProt 154–332 Author chain T； PDBConstruct 2–180； UniProt 154–332 Author chain V； PDBConstruct 2–180； UniProt 154–332 Author chain X； PDBConstruct 2–180； UniProt 154–332 Author chain Z； PDBConstruct 2–180； UniProt 154–332 Author chain b； PDBConstruct 2–180； UniProt 154–332

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	3tcx
Deposition date deposition_date	2011-08-09
Structure title title	Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation
Keywords keywords	Rossmann Fold, Immunoglobulin-Like Fold, Cell Adhesion, Membrane; CELL ADHESION
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.

3tcx__assembly_1__model_1

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

Download this curve (.dat)

3tcx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3tcx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.63 Å
Rg (electron density)	19.68 Å
Total Rg	20.62 Å
Atom count	2095
Residues	265
Excluded volume	37775 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3tcx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3tcx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3tcx__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3tcx__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3tcx__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3tcx__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3tcx__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3tcx__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3tcx__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3tcx__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3tcx__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3tcx__assembly_12__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`3tcx__assembly_13__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`3tcx__assembly_14__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Intercellular adhesion molecule 1
Molecular weight formula_weight	9214.6 kDa
Mutation mutation	T2V, I10T, T23A, P38V, P63V, S67A, T78A
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q,S,U,W,Y,a
Atom count atom_count	29330

MVSVSPSKVTLPRGGSVLVTCSASCDQPKLLGIETPLVKKELLLPGNNRKVYELSNVQEDSQVMCYANCPDGQSTAKAFLTVYWT

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

Entity 2 Entity 2 polymer

Description description	Integrin alpha-L
Molecular weight formula_weight	20622.6 kDa
Mutation mutation	F265S
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R,T,V,X,Z,b

MNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKWKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHSQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKIY

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

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	14

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6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id	3tcxA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxM00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxO00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxP00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxQ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxR00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxS00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxT00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxU00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxV00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxW00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxX00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxY00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxZ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	3tcxa00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3tcxb00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

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Unit-cell length a length_a	104.041 Å
Unit-cell length b length_b	166.334 Å
Unit-cell length c length_c	299.372 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	56

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	49.540 Å
R factor r_factor	0.2185
R_work r_work	0.2176
R_free r_free	0.2336

Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation

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

Intercellular adhesion molecule 1

State in the Current Structure

Other States of the Same Protein in the Database

Integrin alpha-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

3tcx__assembly_1__model_1

3tcx__assembly_1__model_1 | I(q)

3tcx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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 non-polymer

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

7. Citations (1)

Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain of Native C-Terminal Helix Conformation

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

Intercellular adhesion molecule 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

Integrin alpha-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

3tcx__assembly_1__model_1

3tcx__assembly_1__model_1 | I(q)

3tcx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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 non-polymer

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

7. Citations (1)